After Gamble, Bauer, Greenbaum & Jackman, 2008,and Pyron, Burbrink & Wiens, 2013, with fossil species from Alifanov, 2000, and Gao & Norell, 2000, and Recent species from Welch, 1994, and Uetz, Etzold & Chenna, 1995-2018 [“The Reptile Database”]

Families

<==o Gekkota Cuvier, 1817 sensu stricto [Nyctisauria] (gekkomaiset liskot)
   |?-o †Cadurcogekko Hoffstetter, 1946; U.Eoc. or L.Olig. Eu.
   |  |-- †C. piveteaui Hoffstetter, 1946
   |  `-- †C. verus Bolet, Daza, Augé & Bauer, 2015 [Cadurcogekko rugosus Augé, 2005]
   |?-o †Gerandogekko Hoffstetter, 1946 Mioc. Eu.
   |  |-- †G. gaillardi Hoffstetter, 1946
   |  `-- †G. arambourgi Hoffstetter, 1946
   |?- †Gobekko cretacius Borsuk-Bialynicka, 1990; U.Cret. EAs.
   |?- †Hoburogekko sukhanovi Alifanov, 1989; L.Cret. EAs.
   |?- †Laonogekko lefevrei Augé, 2005; L.Eoc. WEu.
   |?- †Myrmecodaptria microphagosa Gao & Norell, 2000; U.Cret. EAs.
   |?- †Palaeogekko risgoviensis Schleich, 1987; M.Mioc. CEu.
   |?- †Rhodanogekko vireti Hoffstetter, 1946; U.Eoc. Eu.
   |--o “Pygopodoidea” [Pygopodidae sensu Welch, 1994] (eväjalkaliskot)
   |  |-- Diplodactylidae
   |  `--+-- Carphodactylidae
   |     `-- Pygopodidae
   `--+--o Eublepharoidea
      |  `-- Eubleparidae
      `--o Gekkonoidea
         |-- Sphaerodactylidae Underwood, 1954
         `--+-- Phyllodactylidae
            `-- Gekkonidae Gray, 1825 (gekot)

with genera:

<==o Gekkota Cuvier, 1817 sensu stricto [Nyctisauria] (gekkomaiset liskot)
   |?-o †Cadurcogekko Hoffstetter, 1946; U.Eoc. or L.Olig. Eu.
   |  |-- †C. piveteaui Hoffstetter, 1946
   |  `-- †C. verus Bolet, Daza, Augé & Bauer, 2015 [Cadurcogekko rugosus Augé, 2005]
   |?-o †Gerandogekko Hoffstetter, 1946 Mioc. Eu.
   |  |-- †G. gaillardi Hoffstetter, 1946
   |  `-- †G. arambourgi Hoffstetter, 1946
   |?- †Gobekko cretacius Borsuk-Bialynicka, 1990; U.Cret. EAs.
   |?- †Hoburogekko sukhanovi Alifanov, 1989; L.Cret. EAs.
   |?- †Laonogekko lefevrei Augé, 2005; L.Eoc. WEu.
   |?- †Myrmecodaptria microphagosa Gao & Norell, 2000; U.Cret. EAs.
   |?- †Palaeogekko risgoviensis Schleich, 1987; M.Mioc. CEu.
   |?- †Rhodanogekko vireti Hoffstetter, 1946; U.Eoc. Eu.
   |--o “Pygopodoidea” [Pygopodidae sensu lato (Welch, 1994)] (eväjalkaliskot)
   |  |--o Diplodactylidae
   |  |  |--+-- Pseudothecadactylus
   |  |  |  `--+== Rhacodactylus
   |  |  |     `--+-- Oedodera
   |  |  |        `--+-- Deirogekko
   |  |  |           `--+==o Bavayia
   |  |  |              |-- Paniegekko madjo (Bauer, Jones & Sadlier, 2000)
   |  |  |              `--+-- Correlophus
   |  |  |                 `--+== Eurydactylodes
   |  |  |                    `-- Mniarogekko
   |  |  `--+-- Crenadactylus
   |  |     `--+--+--+-- Hoplodactylus
   |  |        |  |  `-- Woodworthia
   |  |        |  `--+--+-- Dactylocnemis
   |  |        |     |  `-- Toropuku
   |  |        |     `--+-- Mokopirirakau
   |  |        |        `--+-- Tukutuku
   |  |        |           `-- Naultinus
   |  |        `--+--+-- Nebulifera
   |  |           |  `-- Amalosia
   |  |           `--+-- Hesperoedura reticulata (Bustard, 1969) [Oedura reticulata Bustard, 1969]
   |  |              `--+--+-- Oedura
   |  |                 |  `-- Strophurus
   |  |                 `--+-- Diplodactylus
   |  |                    `--+-- Rhynchoedura
   |  |                       `-- Lucasium
   |  `--+--o Carphodactylidae
   |     |  |--+-- Phyllurus
   |     |  |  `-- Saltuarius
   |     |  `--+-- Orraya
   |     |     `--+-- Carphodactylus
   |     |        `--+-- Uvidicolus
   |     |           `--+-- Underwoodisaurus
   |     |              `-- Nephrurus
   |     `--o Pygopodidae
   |        |-- Delma [incl. Aclys]
   |        `--+--+-- Ophidiocephalus
   |           |  `-- Lialis
   |           `--+-- Pletholax
   |              `--+-- Aprasia
   |                 `--+-- Paradelma
   |                    `-- Pygopus
   `--+--o Eublepharoidea
      |  `--o Eubleparidae
      |     |--o ?Aeluroscalabotinae
      |     |  |-- Aeluroscalabotes
      |     |  `-- Coleonyx
      |     `--o ?Eublepharinae
      |        |-- Goniurosaurus
      |        `--+-- Eublepharis
      |           `--+-- Hemitheconyx
      |              `-- Holodactylus
      `--o Gekkonoidea
         |--o Sphaerodactylidae Underwood, 1954
         |  |--+-- Pristurus Rüppell, 1835
         |  |  `--+--+-- Quedenfeldtia Boettger, 1883 (atlas day geckos; atlaksenpäivägekot)
         |  |     |  `-- Aristelliger Cope, 1862
         |  |     `--+-- Teratoscincus Strauch, 1863 [Teratoscincinae]
         |  |        `--+-- Saurodactylus fasciatus 
         |  |           `-- Euleptes europaea (Gené, 1839) Fitzinger, 1843 [= Phyllodactylus europaeus (lehtivarvasgekko)??]
         |  `--+-- Saurodactylus mauritanicus
         |     `--+-- Chatogekko amazonicus (Andersson, 1918) Gamble, Daza, Colli, Vitt & Bauer, 2011
         |        `--+--+-- Lepidoblepharis Peracca, 1897
         |           |  `-- Gonatodes Fitzinger, 1843
         |           `--+-- Coleodactylus Parker, 1926
         |              `--+-- Pseudogonatodes Ruthven, 1915
         |                 `-- Sphaerodactylus Wagler, 1830
         `--+-- Phyllodactylidae
            `-- Gekkonidae Gray, 1825 (gekot)

            `-- o Gekkonidae
            |?- Afrogecko
            |?- Cryptactites peringueyi
            |?- Cyrtodactylus
            |?- Dixonius
            |?- Goggia
            |?- Haemodracon
            |--o Gekkonini
            |  |-- Agamura
            |  |-- Ailuronyx
            |  |-- Alsophylax
            |  |-- Blaesodactylus Boettger, 1893 [Homopholis]
            |  |-- Bogertia lutzae Loveridge, 1941
            |  |-- Briba brasiliana Amaral, 1935
            |  |-- Bunopus
            |  |-- Calodactylus [not recognized by the Reptile Database]
               |-- Carinatogecko
            |  |-- Cnemaspis
            |  |-- Cosymbotes [not recognized by the  Reptile Database]
            |  |-- Crossobamon
            |  |-- Cyrtopodion
            |  |-- Dravidogecko [not recognized by the  Reptile Database]
            |  |-- Geckolepis
            |  |-- Gehyra
            |  |-- Gekko
            |  |-- Gonydactylus
            |  |-- Gymnodactylus
            |  |-- Hemidactylus
            |  |-- Hemiphyllodactylus
            |  |-- Heteronotia
            |  |-- Homopholis [not recognized by the Reptile Database]
            |  |-- Lepidodactylus
            |  |-- Luperosaurus
            |  |-- Lygodactylus Gray, 1864 [incl. Millotisaurus Pasteur, 1962] (African Dwarf Geckos)
            |  |-- Perochirus
            |  |-- Phyllopezus
            |  |-- Pseudogekko
            |  |-- Ptychozoon
            |  |-- Stenodactylus
            |  |-- Tenuidactylus
            |  |-- Teratolepis
            |  |-- Thecadactylus Houttuyn, 1782
            |  |-- Tropiocolotes
            |  |-- Urocotyledon
            |  `-- Uroplatus
            `--o Ptyodactylini [27/216]
               |-- Afroedura Loveridge, 1944
               |-- Asaccus Dixon & Anderson, 1973
               |-- Asiocolotes Golubev, 1984 [2]
               |-- Christinus Wells & Wellington, 1984 [2]
               |-- Ebenavia Boettger, l878 [2]
               |-- Geckoella Gray, 1867 [5]
               |-- Homonota Gray, 1845 [9]
               |-- Mediodactylus Szczerbak & Golubev, 1977 [7]
               |-- Microgecko Nikolsky, 1901 [3]
               |-- Microscalabotes bivittis Boulenger, 1883 or Peters, 1883
               |-- Nactus Kluge, 1983 [6]
               |-- Narudasia festiva Methuen & Hewitt, 1914
               |-- Paragehyra Angel, 1929 [2]
               |-- Paroedura Günther, 1879 [15]
               |-- Phelsuma Gray, 1825 [39]
               |-- Phyllodactylus Gray, 1828 [46]
               |-- Ptenopus Gray, 1865 [3]
               |-- Ptyodactylus Goldfuss, 1820 [6]
               |-- Saurodactylus Fitzinger, 1843 [2]
               `--o Pachydactylus -group
                  |-- Chondrodactylus angulifer Peters, 1870
                  |-- Colopus wahlbergii Peters, 1869
                  |-- Geckonia chazaliae Mocquard, 1895
                  |-- Tarentola Gray, 1825 [20]
                  |-- Pachydactylus Wiegmann, l834 [incl. Elasmodactylus Boulenger] [34]
                  |-- Palmatogecko Andersson, 1908 [incl. Kaokogecko Steyn & Haacke, 1966, non Xaokogecko (lapsus calami)] [2]
                  `-- Rhoptropus Peters, 1869 (Namid day geckos; namibinpäivägekot)? [7]

After Pyron, Burbrink & Wiens, 2013

<==o Gekkota
    |--+-- Diplodactylidae
    |  `--+-- Carphodactylidae
    |     `-- Pygopodidae
    `--+-- Eublepharidae
       `--+-- Sphaerodactylidae
          `--+-- Phyllodactylidae
             `-- Gekkonidae

Reference(s):

  • Pyron, R., Burbrink, F. & Wiens, J., 2013: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.
    –BMC Evolutionary Biology: Vol. 13, #1, Art. nr. 93, pp. 1-53 [doi: 10.1186/1471-2148-13-93]

Reference(s):