After Šlechtová, Bohlen & Perdices, 2008 (fig. 4 & 5), with Recent species from Froese & Pauly, 2001 [“The Fishbase”] and Kottelat, 2012

<==o Cobitidae Swainson, 1838 [Cobitidae Swainson, 1838; Acanthopsides Heckel & Kner, 1858; Misgurninae Fowler, 1905] (cobitine loaches; piikkinuoliaiset; “rantaneulat”)
   |--o Lepidocephalus Bleeker, 1858
   |  |?- L. caudofurcatus Tilak & Husain, 1978 (Tilak loach)
   |  |-- L. macrochir (Bleeker, 1854) [Cobitis macrochir Bleeker, 1854; Lepidocephalichthys pallens Vaillant, 1902; Acanthophthalmus pahangensis de Beaufort, 1933]
   |  `?- L. spectrum Roberts, 1989
   |--+-- Neoeucirrhichthys maydelli Banarescu & Nalbant, 1968 (Goalpara loach)
   |  `-- Canthophrys gongota (Hamilton, 1822) Swainson, 1838 [Cobitis gongota Hamilton, 1822; Cobitis cucura Hamilton, 1822; Cobitis oculata M'Clelland, 1839; Canthophrys albescens Swainson, 1838; Somileptus bispinosa Swainson, 1838; ?Cobitis amnicola Valenciennes, in Cuvier & Valenciennes, 1846] (Gongota loach)
   |--o Lepidocephalichthys Bleeker, 1863 [taxonomic history]
   |  |?- L. alkaia Havird & Page, 2010
   |  |?- L. annandalei Chaudhuri, 1912 [taxonomic history] (Annandale loach)
   |  |?- ?L. arunachalensis (Datta & Barman, 1984) [taxonomic history]
   |  |?- L. barbatuloides (Bleeker, 1851) [taxonomic history]
   |  |?- ?L. birmanicus (Rendahl, 1948)
   |  |?- L. coromandelensis (Menon, 1992) [taxonomic history]
   |  |?- L. furcatus (de Beaufort, 1933) [taxonomic history]
   |  |?- ?L. goalparensis Pillai & Yazdani, 1976 [taxonomic history] (Pillai loach)
   |  |?- L. irrorata Hora, 1921 [taxonomic history] (Loktak loach)
   |  |?- L. jonklaasi (Deraniyagala, 1956) [taxonomic history] (Jonklaas's loach)
   |  |?- L. kranos Havird & Page, 2010
   |  |?- L. lorentzi (Weber & de Beaufort, 1916) [taxonomic history]
   |  |?- L. micropogon (Blyth, 1860) [taxonomic history]
   |  |?- L. tomaculum Kottelat & Lim, 1992
   |  |?- L. zeppelini Havird & Tangjitjaroen, in Havind, Page, Tangjitjaroen, Vidthayanon, Grudpan & Udduang, 2010
   |  |-- L. thermalis (Valenciennes, 1846) [taxonomic history] (Common spiny loach; täplänuoliainen)
   |  `--+-- L. hasselti (Valenciennes, 1846) [taxonomic history]
   |     `--+-- L. guntea (Hamilton, 1822) (Guntea loach)
   |        `-- L. berdmorei (Blyth, 1860) [taxonomic history] (Burmese loach)
   `?-+--+--o Acantopsis van Hasselt, 1823 [Acanthopsis van Hasselt, 1824; ?Aperioptus Richardson, 1848; Prostheacanthus Blyth, 1860] (kärsänuoliaiset)
      |  |  |-- A. dialuzona Van Hasselt, 1823 [Acantopsis Dialuzona Van Hasselt, 1823; ?Aperioptus pictorius Richardson, 1848; Acantopsis biaculeata Rüppell, 1852; Cobitis choirorhynchos Bleeker, 1854; Cobitis macrorhynchos Bleeker, 1854] (Horseface loach; kärsänuoliainen, hevosnuoliainen)
      |  |  |-- A. octoactinotos Siebert, 1991
      |  |  |-- A. spectabilis Blyth, 1860 [Prostheacanthus spectabilis Blyth, 1860; ?Acantopsis multistigmatus Vishwanath & Laisram, 2005]
      |  |  `-- A. thiemmedhi Sontirat, 1999 [A. thiemmedhi Sontirat, 1997 (nomen nudum)]
      |  `==o Acanthopsoides Fowler, 1934 [Neacanthopsis Smith, 1945]
      |     |?- A. delphax Siebert, 1991
      |     |?- A. gracilis Fowler, 1934 (pikkukärsänuoliainen)
      |     |?- A. molobrion Siebert, 1991
      |     |--+-- A. gracilentus (Smith, 1945) [Neacanthopsis gracilentus Smith, 1945; Acanthopsoides namromensis Nguyen, 2005]
      |     |  `-- A. hapalias Siebert, 1991
      |     `--+-- A. robertsi Siebert, 1991
      |        `--o Kottelatlimia Nalbant, 1994 [Lepidocephalichthys Bleeker, 1863 in partim]
      |           |?- K. hipporhynchos Kottelat & Tan, 2008
      |           |-- K. katik (Kottelat & Lim, 1993) [Lepidocephalichthys katik Kottelat & Lim, 1993]
      |           `-- K. pristes(Roberts, 1989) [Lepidocephalichthys pristes Roberts, 1989]
      `?-+-- Pangio Blyth, 1860 [incl. Eucirrichthys Perugia, 1892; Cobitophis Myers, 1927] [taxonomic history] (coolie-loaches; piikkisilmät)
         `--+-- Microcobitis misgurnoides (Rendahl, 1944) Bohlen & Harant, 2011 [Cobitis misgurnoides Rendahl, 1944; ?Cobitis nuicocensis Nguyen & Vo, in Nguyen, 2005]
            `?-+--o Sabanejewia Vladykov, 1829
               |  |?- S. balcanica (Karaman, 1922) [Cobitis balcanica Karaman, 1922; Cobitis montana Vladykov, 1925; Cobitis aurata balcanica natio radnensis Jaszfalusi, 1951; Cobitis aurata balcanica morpha elongata Oliva, Balon & Franck, 1952; Cobitis aurata balcanica morpha elata Oliva, Balon & Franck, 1952; Cobitis aurata radnensis Banarescu, Müller & Nalbant, 1960; Cobitis aurata bosniaca Karaman, 1963; ?Sabanejewia aurata doiranica Economidis, 1995 (nomen nudum); ?Sabanejewia aurata thrakica Economidis, 1995 (nomen nudum); ?Sabanejewia aurata doiranica Economidis & Nalbant, 1997; Sabanejewia aurata thrakica Economidis & Nalbant, 1997]
               |  |?- S. baltica Witkowski, 1994 [S. aurata baltica Witkowski, 1994]
               |  |?- S. caspia (Eichwald, 1838) [Cobitis caspia Eichwald, 1838] (Caspian spined loach)
               |  |?- S. caucasica (Berg, 1906) [Cobitis caucasica Berg, 1906]
               |  |?- S. kubanica Vasil'eva & Vasil'ev, 1988 [S. aurata kubanica Vasil'eva & Vasil'ev, 1988]
               |  |?- S. vallachica (Nalbant, 1957) [Cobitis aurata vallachica Nalbant, 1957]
               |  |-- S. larvata (De Filippi, 1859) [Cobitis larvata De Filippi, 1859; Cobitis taenia var. conspersa Cantoni, 1882]
               |  `--+-- S. romanica (Bacescu, 1943) [Cobitis caspia romanica Bacescu, 1943]
               |     `--+-- S. bulgarica (Drensky, 1928) [Cobitis bulgarica Drensky, 1928; Cobitis albicoloris Chichkoff, 1932; Cobitis taenia tesselatus Pietschmann, 1937]
               |        `--o S. aurata (De Filippi, 1863) [Cobitis aurata De Filippi, 1863; Cobitis hohenackeri Kessler, 1877; ?Cobitis aralensis Kessler, 1877] (Golden spined loach)
               |           |-- S. a. aurata (De Filippi, 1863)
               |           `-- S. a. aralensis (Kessler, 1877) [?Cobitis aralensis Kessler, 1877] (Aral spined loach)
               `--+--+--o Koreocobitis Kim, Park & Nalbant, 1997 [Cobitis in partim]
                  |  |  |-- K. rotundicaudata (Wakiya & Mori, 1929) [Cobitis rotundicaudata Wakiya & Mori, 1929]
                  |  |  `-- K. naktongensis Kim, Park & Nalbant, 2000
                  |  `--+-- Paramisgurnus dabryanus Dabry de Thiersant, 1872 [Paramisgurnus dabryanus Sauvage, 1878; Misgurnus mizolepis Günther, 1888;Misgurnus oligolepos Chen, Shen & Li, 1994]
                  |     `--+-- Misgurnus fossilis (Linnaeus, 1758) [taxonomic history] (euroopanmutakala, barometrikala; Weatherfish)
                  |        `--+-- Misgurnus sp.1
                  |           `-- Misgurnus anguillicaudatus (Cantor, 1842) A [taxonomic history] (aasianmutakala, “kiinanmonni”; Oriental weatherfish) [polyphyletic]
                  `--+--+--+-- Iksookimia choii (Kim & Son, 1984) (Choi's spiny loach)
                     |  |  `--+-- Cobitis melanoleuca Nichols, 1925 [Cobitis taenia melanoleuca Nichols, 1925]
                     |  |     |?- Cobitis gladkovi Vasil'eva & Vasil'ev, 2008 [Cobitis melanoleuca gladkovi Vasil'eva & Vasil'ev, 2008]
                     |  |     `?- Cobitis sibirica Gladkov, 1935 [Cobitis taenia sibirica Gladkov, 1935; Cobitis taenia granoei Rendahl, 1935; Cobitis taenia sibirica morpha elongata Berg, 1949; Cobitis granoei olivai Nalbant, Holcik & Pivnicka, 1970; Cobitis melanoleuca granoei Vasil'eva & Vasil'ev, 2008] (Siberian spiny loach)
                     |  `--+-- Niwaella delicata (Niwa, 1937) Nalbant, 1963 [Cobitis delicata Niwa, 1937] [Niwaëlla Nalbant, 1963] [polyphyletic]
                     |     `--+-- Cobitis striata Ikeda, 1936 [Cobitis taenia striata Ikeda, 1936]
                     |        `-- Cobitis biwae Jordan & Snyder, 1901 [Cobitis taenia japonica Temminck & Schlegel, 1846; Cobitis Schlegeli Bleeker, 1863 (nomen oblitum)]
                     `--+--+-- Iksookimia pacifica (Kim, Park & Nalbant, 1999) [Cobitis pacifica Kim, Park & Nalbant, 1999]
                        |  `--+-- Iksookimia pumila (Kim & Lee, 1987) [Cobitis koreensis pumilus Kim & Lee, 1987]
                        |     `-- Iksookimia koreensis (Kim, 1975) [Cobitis koreensis Kim, 1975]
                        `--+--+-- ?Niwaella sp. cf. N. laterimaculata
                           |  |?- ?Niwaella laterimaculata (Yan & Zheng, 1984) [Cobitis laterimaculata Yan & Zheng, 1984]
                           |  |?- ?Niwaella longibarba Chen & Chen, 2005
                           |  `?- ?Niwaella xinjiangensis Chen & Chen, 2005
                           `?-+--+-- Cobitis taenia Linnaeus, 1758 [Cobitis Taenia Linnaeus, 1758; Cobitis spilura Holandre, 1837; Cobitis taenioides Bacescu & Maier, 1969; Cobitis taenia taenia] (rantaneula; Spined loach)
                              |  `?-+-- Cobitis elazigensis Coad & Sarieyyüpoglu, 1988 [=? C. simplicispina Hankó, 1924 (Erkakan et al., 1999)]
                              |     `--o Cobitis (Iberocobitis) Bacescu, 1962
                              |        |-- C. (I.) maroccana Pellegrin, 1929 [Cobitis taenia var. maroccana Pellegrin, 1929]
                              |        |-- C. (I.) paludica (de Buen, 1930) [Acanthopsis taenia forma paludica de Buen, 1930; Cobitis taenia paludicola Berg, 1932; Cobitis taenia haasi Klausewitz, 1955; ?Cobitis vitoriae Fernandez de la Cigoña Núñez & Ferreira, 1996; ?Cobitis victoriae Fernandez de la Cigoña Núñez, 1999]
                              |        `-- C. (I.) vettonica Doadrio & Perdices, 1997
                              `--+-- Cobitis rara Chen , 1981
                                 `?-+--+-- Misgurnus anguillicaudatus (Cantor, 1842) B [taxonomic history] (Oriental weatherfish; aasianmutakala, “kiinanmonni”) [polyphyletic]
                                    |  `--+-- Misgurnus sp.2
                                    |     `--+-- Misgurnus sp.3
                                    |        `-- Misgurnus mohoity [incl. Misgurnus bipartitus sensu Kottelat, 2012] [taxonomic history]
                                    `?-+?-+?- Cobitis bilineata Canestrini, 1866 [Cobitis taenia var. bilineata Canestrini, 1866; Cobitis taenia var. puta Cantoni, 1882; Cobitis taenia var. septa Cantoni, 1882]
                                       |  `?- Cobitis elongata Heckel & Kner, 1858
                                       `--+-- Cobitis lutheri Rendahl, 1935 [Cobitis taenia lutheri Rendahl, 1935] (Luther's spiny loach)
                                          `--+--+-- Iksookimia yongdokensis Kim & Park, 1997
                                             |  `-- Iksookimia longicorpus (Kim, Choi & Nalbant, 1976) [Cobitis longicorpus (Kim, Choi & Nalbant, 1976]
                                             `?-o Kichulchoia Kim, Park & Nalbant, 1999 [Choia Kim, Park & Nalbant, 1997 non Choia Walcott, 1920 (a fossil sponge (Porifera))]
                                                |-- K. brevifasciata Kim & Lee, 1995 [Niwaella brevifasciata Kim & Lee, 1995]
                                                `-- K. multifasciata (Wakiya & Mori, 1929) [Cobitis multifasciata Wakiya & Mori, 1929; Niwaella multifasciata (Wakiya & Mori, 1929)]

Untreated Cobitids

    Bibarba bibarba Chen & Chen, 2007
    Iksookimia Nalbant, 1993
        I. hugowolfeldi Nalbant, 1993
    Misgurnus Lacepčdé [La Cepčde], 1803 [taxonomic history] (mutakalat) [polyphyletic]
        M. buphoensis Kim & Pak, 1995 [taxonomic history]
        M. multimaculatus Rendahl, 1944 [taxonomic history]
        M. nikolskyi Vasil'eva, 2001 [taxonomic history]
        M. tonkinensis Rendahl, 1937 [taxonomic history]
    Theriodes sandakanensis (Inger & Kong, 1962) Kottelat, 2012 [Acanthophthalmus sandakanensis Inger & Kong, 1962; Lepidocephalichthys sandakanensis (Inger & Kong, 1962); Pangio? sandakanensis (Inger & Kong, 1962) sensu Havird & Page, 2010]
    Paralepidocephalus Tchang, 1935
        ?P. guishanensis Li, 2004 [Paralepidcephalus [sic] guishanensis Li, 2004]
        P. yui Tchang, 1935
    'Protocobitis' polylepis Zhu, Lü, Yamng & Zhang, 2008; Kottelat, 2012
    Protocobitis typhlops Yang & Chen, 1993 [Protocobitis typhlops Yang, Chen & Lan, 1994]

    Cobitis Linnaeus, 1758 [Acantophthalmus van Hasselt, 1823; Acanthophthalmus van Hasselt, 1823; ?Acanthopsis Agassiz, 1832; Cobitinula Hankó, 1924; Acanestrinia Bacescu, 1962; Bicanestrina Bacescu, 1962; Iberocobitis Bacescu, 1962; Beyshehiria Erk'akan, Atalay-Ekmekçi & Nalbant, 1999] Olig. R. Eu. R. As. NAf.
        †G. centrochir
        C. amphilekta Vasil'eva & Vasil'ev, 2012
        C. arachthosensis Economidis & Nalbant, 1996 [Cobitis hellenica arahthosensis Economidis, 1991 (nomen nudum); Cobitis arachthosensis Economidis & Nalbant, 1996]
        C. bilseli Battalgil, 1942
        C. calderoni Bacescu, 1962 [Cobitis Calderóni Bacescu, 1962]
        C. choii Kim & Son, 1984
        ?C. caucasica Berg, 1906 (Ciscaucasian spined loach)
        ?C. conspersa Cantoni, 1882
        C. dalmatina Karaman, 1928 [Cobitis taenia dalmatina Karaman, 1928]
        C. dolichorhynchus Nichols, 1918
        C. elongatoides Bacescu & Maier, 1969 [Cobitis taenia var. elongatoďdes Bacescu, 1962; Cobitis taenia elongatoides Bacescu & Maier, 1969; Cobitis taenia danubialis Nalbant, 1993; Cobitis megaspila Nalbant, 1993]
        C. evreni Erk'akan, Özeren & Nalbant, 2008
        C. fahifeae Erk'akan, Atalay-Ekmekçi & Nalbant, 2008 [Cobitis fahifae Erk'akan, Atalay-Ekmekçi & Nalbant, 2008 (lapsus calami)]
        C. faridpaki Mousevi-Sabet, Vasil'eva, Vatandoust & Vasil'ev, 2011
        ?C. haasi Klausewitz, 1955
        C. hankugensis Kim, Park, Son & Nalbant, 2003
        C. hellenica Economidis & Nalbant, 1997 [Cobitis hellenica Economidis, 1991 (nomen nudum)]
        C. illyrica Freyhof & Stelbrink, 2007
        C. jadovaensis Mustafic & Mrakovcic, in Mustafic, Marcic, Dublic, Mrakovcic, Caleta, Zanella, Buj, Podnar & Dolenec, 2008
        C. kellei Erk'akan, Atalay-Ekmekçi & Nalbant, 1998
        C. keyvani Mousavi-Sabet, Yerli, Vatandoust, Özeren & Moradkhani, 2012
        C. laoensis (Sauvage, 1878) [Misgurnus laoensis Sauvage, 1878; ?Cobitis longitaeniatus Ngo, 2008; ?Cobitis longitaenia Ngo, 2008 (lapsus calami); ?Cobitis phongnhaensis Ngo, 2008]
        ?C. lebedevi Vasil'eva & Vasil'ev, 1985 [=? Cobitis choii Kim & Son, 1984 (Bogutskaya et al., 2008)]
        C. levantina Krupp & Moubayed, 1992
        C. linea (Heckel, 1846-49) [Acanthopsis linea Heckel, 1846-49]
        C. macrostigma Dabry de Thiersant, 1872
        C. matsubarae Okada & Ikeda, 1939 [Cobitis taenia matsubarae Okada & Ikeda, 1939]
        C. meridionalis Karaman, 1924 [Cobitis taenia meridionalis Karaman, 1924]
        C. microcephala Chen & Chen, 2011
        C. multimaculata Chen & Chen, 2011
        C. narentana Karaman, 1928 [Cobitis taenia narentana Karaman, 1928]
        C. ohridana Karaman, 1928 [Cobitis taenia ohridana Karaman, 1928]
        C. phrygica Battalgazi, 1944 [Cobitis Battalgili Bacescu, 1962] [=? Cobitis simplicispina Hankó, 1924 (Erkakan et al., 1999)]
        C. pontica Vasil'eva & Vasil'ev, 2006
        C. puncticulata Erk'akan, Atalay-Ekmekçi & Nalbant, 1998
        C. punctilineata Economidis & Nalbant, 1997 [C. punctilineata Economidis, 1991 (nomen nudum)]
        C. satunini Gladkov, 1985 [Cobitis taenia satunini Gladkov, 1985]
        C. shikokuensis suzawa, 2006
        C. simplicispina Hankó, 1924
        C. sinensis Sauvage & Dabry de Thiersant, 1874
        C. splendens Erk'akan, Atalay-Ekmekçi & Nalbant, 1998
        C. stephanidisi Economidis, 1992 [C. stephanidisi Economidis, 1991 (nomen nudum); C. stephanidisi Economidis & Nalbant, 1997]
        C. strumicae Karaman, 1955 [Cobitis taenia strumicae Karaman, 1955; Cobitis peschevi Sivkov & Dobrovolov, 1984; Cobitis rhodopensis Vassilev, 1998]
        C. takatsuensis Mizuno, 1970
        C. tanaitica Bacescu & Maier, 1969 [Cobitis taenia tanaitica Bacescu & Maier, 1969; Cobitis rossomeridionalis  Vasil'eva & Vasil'ev, 1998]
        C. taurica Vasil'eva, Vasil'ev, Janko, Ráb & Rábová, in Janko, Vasil'ev, Ráb, Rábová, Šlechtová & Vasil'eva, 2005
        C. tetralineata Kim, Park & Nalbant, 1999
        C. trichonica Stephanidis, 1974
        C. turcica Hankó, 1924 [Cobitis taenia turcica Hankó, 1924; ?Cobitinula anatoliae Hankó, 1924]
        C. vardarensis Karaman, 1928 [Cobitis taenia vardarensis Karaman, 1928; C. vardarensis kurui Erk'akan, Atalay-Ekmekçi & Nalbant, 1998]
        C. ylengensis Ngo, 2003 [?Cobitis squataeniatus Ngo, 2008]
        C. zanandreai Cavicchioli, 1965 [Cobitis taenia zanandreai Cavicchioli, 1965]
        C. zhejiangensis Son & He, 2005
        ?C. arenae (Lin, 1934) [Misgurnus aranae Lin, 1934] (incertae sedis)
        ?C. guttata (Nguyen, 2005) [Acantopsis guttatus Nguyen, 2005] [non Cobitis guttata M'Clelland, 1839] (incertae sedis)
        ?C. longimanus Dybowski, in Sinicyn, 1900 (nomen nudum)
        ?C. lachnostoma (Rutter, 1897) [Acanthopsis lachnostoma Rutter, 1897]
        ?C. poecilopleura Bleeker, 1872 (nomen nudum)
        ?C. yeni Nguyen, 1982 (nomen nudum)

Alternative phylogenies of Cobitidae

After Ramaswami, 1953 [via Šlechtová, Bohlen & Perdices, 2008]

<==o Cobitidae
   |--+-- Cobitis
   |  |-- Misgurnus
   |  `-- Canthophrys
   `--+-- Acantopsis
      |-- Pangio
      `-- Lepidocephalus

After Nalbant, 1963 [via Šlechtová, Bohlen & Perdices, 2008]

<==o Cobitidae
   |-- Enobarbus
   `--+-- Misgurnus
      |--+-- Canthophrys
      |  `--+-- Niwaella
      |     `--+-- Sabanejewia
      |        `-- Cobitis
      `--+--+-- Acantopsis
         |  `-- Acantopsoides
         `--+--+-- Paralepidocephalus
            |  `--+-- Lepidocephalichthys
            |     `-- Lepidocephalus
            `--+-- Eucirrichthys
               `--+-- Cobitophis
                  `-- Pangio

After Sawada, 1982 [via Šlechtová, Bohlen & Perdices, 2008]

<==o Cobitidae
   |--+-- Misgurnus
   |  `-- Pangio
   `--+-- Acantopsis
      `--+-- Niwaella
         `--+-- Acantopsoides
            `--+-- Cobitis
               |-- Iksookimia
               |-- Lepidocephalichthys
               `-- Sabanejewia

After Nalbant, 1994 [via Šlechtová, Bohlen & Perdices, 2008]

<==o Cobitidae
   |-- Enobarbus
   |-- Canthophrys
   |-- Kottelatiimia
   `--+--+-- Misgurnus
      |  |--+-- Acantopsis
      |  |  `-- Acantopsoides
      |  `--+-- Cobitis
      |     |-- Iksookimia
      |     |-- Niwaella
      |     |-- Paralepidocephalus
      |     `-- Sabanejewia
      `--+--+-- Eucirrichthys
         |  `-- Pangio
         `--+-- Neoeucirrichthys
            `--+-- Lepidocephalichthys
               `-- Lepidocephalus

Reference(s):