Higher Taxa in Extant Reptiles

Order Testudines - Turtles (phylogeny [6MB] -- revised after Thomson 2021 [note 1])

Suborder Cryptodira

Superfamily Testudinoidea

Superfamily Trionychoidea (= Trionychia)

Superfamily Chelydroidea

Superfamily Chelonioidea

Suborder Pleurodira (phylogeny)

Superfamily (none yet)

  • Family Chelidae (Austro-American Sideneck Turtles) W

Superfamily Pelomedusoidea


Order Rhynchocephalia

Suborder Sphenodontida

Order Squamata (phylogeny of squamata) [2]

Sauria (Lacertilia) - Lizards

Superfamily Iguania [3]

Family Iguanidae s.l. ("Iguanas") [Pleurodonta] with the following families previously treated as subfamilies:

Superfamily Gekkota

Superfamily Scincomorpha (phylogeny after Hedges 2014) [Note 4]

Superfamily Lacertoidea (after Zheng & Wiens 2016) (new!)

Superfamily Diploglossa (note 4); (Anguimorpha: Diploglossa + Platynota + Shinisauroidea)

includes Amphisbaenia (note 2)

Superfamily Platynota (Varanoidea) (note 1)

Superfamily Shinisauroidea

Superfamily Dibamia

Ophidia (Serpentes) - Snakes (phylogeny) [Note 5]

Superfamily Acrochordoidea

Superfamily Uropeltoidea s.l. (Pipe snakes and Shield-tailed snakes)

Superfamily Pythonoidea s.l. (Pythons and relatives)

Superfamily Booidea (preliminarily after Vidal & Hedges 2009)

Superfamily Colubroidea (revised after Zaher et al. 2019)

Superfamily Elapoidea (revised after Zaher et al. 2019)

Superfamily Typhlopoidea (Scolecophidia)

Currently not assigned to any Superfamily:


Order Crocodylia - Crocodiles etc. [7]

Suborder Eusuchia

  • Family Crocodylidae (Crocodylians) W
  • Family Gavialidae or Subfamily Gavialinae (Gharials)
  • Family Alligatoridae (Alligators)
    • Subfamily Alligatorinae
    • Subfamily Caimaninae (Caimans) -- see note [7]


Overall taxonomy originally after

Zug,G.R.; Vitt, L.J. & Caldwell, J.P. (2001)
Herpetology, 2nd ed.
Academic Press San Diego, London, [...]XIV + 630 pp.

Vitt, Laurie J.; Janalee P. Caldwell 2013
Herpetology, Fourth Edition: An Introductory Biology of Amphibians.
Academic Press, 776 pp. [ISBN 978-0123869197] [2014]

Albert, Eva M.; Diego San Mauro, Mario García-París, Lukas Rüber and Rafael Zardoya 2009
Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data.
Gene 441(1-2):12-21

[1] Turtles (especially their phylogeny) after

Thomson, R. C., Spinks, P. Q., & Shaffer, H. B. 2021
A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins.
Proceedings of the National Academy of Sciences, 118(7)

[2] Snakes are nested within lizards, so they technically paraphyletic. Squamata after multiple sources including

Douglas et al. (2006) found that snakes formed a sister clade to amphisbaenians which is rejected by Vidal et al. (2005).

Douglas, D.A.; Janke, A. & Arnason, U. (2006)
A mitogenomic study on the phylogenetic position of snakes.
Zoologica Scripta, 35: 545–558

Gamble, T.; A. M. Bauer, e. Greenbaum & T. R. Jackman (2008)
Out of the blue: a novel, trans-Atlantic clade of geckos (Gekkota, Squamata). Zoologica Scripta 37 (4): 355–366

Goicoechea, N., Frost, D. R., De la Riva, I., Pellegrino, K. C. M., Sites, J., Rodrigues, M. T. and Padial, J. M. (2016)
Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment.
Cladistics, doi: 10.1111/cla.12150

Harris, D. J., Marshall, J.C. & Crandall, K.A. (2001)
Squamate relationships based on C-mos nuclear DNA sequences: increased taxon sampling improves bootstrap support.
Amphibia-Reptilia 22 (2): 235-242

Kumazawa, Y. (2007)
Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations.
Gene 388: 19-26

Pyron, R.A.; Frank T Burbrink, John J Wiens 2013
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.
BMC Evol Biol 13: 93

Townsend, T. M., A. Larson, E. Louis, J. R. Macey. 2004. Molecular phylogentics of Squamata: The position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Systematic Biology, 53(5):1-23.

Vidal, Nicolas and S. Blair Hedges (2005)
The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes.
Comptes Rendus Biologies 328 (10-11): 1000-1008

Hedges, S.B. 2014
The high-level classification of skinks (Reptilia, Squamata, Scincomorpha).
Zootaxa 3765 (4): 317–338

Zheng, Yuchi; John J. Wiens 2016
Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species.
Molecular Phylogenetics and Evolution 94: 537–547, doi:10.1016/j.ympev.2015.10.009

Zheng & Wiens 2016 include Amphisbaenians in Lacertoidea, see their phylogeny.

[3] Iguania after

Frost, D.R.; Etheridge, R.; Janies, D. & Titus, T.A. (2001)
Total evidence, sequence alignment, evolution of Polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguania).
American Museum Novitates 3343: 38 pp.
[4]: Scincomorpha partly after Hedges 2014:

Hedges, S.B. 2014
The high-level classification of skinks (Reptilia, Squamata, Scincomorpha).
Zootaxa 3765 (4): 317–338

but see also Squamate phylogeny (Zheng & Wiens 2016) and Shea 2021 who moved many (sub-) families to tribus level:

Shea, G. M. (2021) Nomenclature of supra-generic units within the Family Scincidae (Squamata). Zootaxa 5067 (3): 301–351

Vidal, N. & Hedges, S.B. (2009) The molecular evolutionary tree of lizards, snakes, and amphisbaenians. Comptes Rendus Biologies, 332: 129–139; doi:10.1016/j.crvi.2008.07.010

Anguidae subdivided into Anguinae and Gerrhonotinae following Pyron et al. 2013. Anguidae and Diploglossidae separated following Vitt & Caldwell 2013. Anniellinae (instead of Anniellidae) fide Zheng & Wiens 2016.

Sánchez-Martínez, Paola María; Martha Patricia Ramírez-Pinilla and Daniel Rafael Miranda-Esquivel (2007)
Comparative histology of the vaginal–cloacal region in Squamata and its phylogenetic implications.
Acta Zoologica (Stockholm) 88: 289–307

Anguimorpha after Zheng & Wiens 2016

[5] Snakes mainly after

Pyron, R.A., et al. (2010) The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol. Phylogenet. Evol. (2010), doi:10.1016/j.ympev.2010.11.006

Lee, Michael S. Y.; Andrew F. Hugall, Robin Lawson & John D. Scanlon (2007)
Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses.
Systematics and Biodiversity 5 (4): 371–389

Vidal, N., Delmas, A.S., David, P., Cruaud, C., Couloux, A., Hedges, S.B. (2007). The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes. Comptes Rendus Biologies 330: 182-187

Vidal et al. (2007) The higher-level relationships of alethinophidian snakes inferred from seven nuclear and mitochondrial genes. In: Henderson, R.W., Powell, R., (eds). Biology of the Boas and Pythons, Eagle Mountain Publ., Eagle Montain, Utah. Pp. 27-33.

Vidal et al. (2005, 2007) and other authors suggested various conflicting trees of different topology. While some trees revealed some interesting relationships, such as the Anguidae forming a clade with the Helodermatidae and Varanidae (forming the Anguimorpha), they often lacked certain families (such as the Anniellidae, Xenosauridae etc.).

Zaher H, Murphy RW, Arredondo JC, Graboski R, Machado-Filho PR, Mahlow K, et al. 2019
Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes).
PLoS ONE 14(5): e0216148

[6] Kelly et al. (2009) split the superfamily Elapoidea into 5 families: Atractaspididae (including Atractaspidinae and Aparallactinae), Lamprophiidae, Prosymnidae, Psammophiidae, Pseudaspididae, Pseudoxyrhophiidae (including Pseudoxyrhophiinae and Amplorhininae). While we follow Pyron et al. (2010) here, you can find Kelly's largely equivalent groups (e.g. their Atractaspididae) in the database (as Atractaspidinae etc).

Kelly, Christopher M. R.; Nigel P. Barker, Martin H. Villet and Donald G. Broadley 2009
Cladistics 25: 38-63

Hydrophiinae after

Strickland, J. L., Carter, S., Kraus, F. and Parkinson, C. L. 2016
Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes, Elapidae), and the evolutionary history of the enigmatic New Guinean elapid Toxicocalamus.
Zoological Journal of the Linnean Society.doi: 10.1111/zoj.12423

The classical separation into sea snakes and terrestrial elapids is not supported by molecular data. While the Hydrophiinae forms a clade, Laticauda is derived from terrestrial elapids. See Lee et al. for details.

Lee, Michael S. Y.; Kate L. Sanders, Benedict King, Alessandro Palci 2016
Diversification rates and phenotypic evolution in venomous snakes (Elapidae)
R. Soc. open sci., DOI: 10.1098/rsos.150277

Viperidae after

Alencar, Laura R.V.; Tiago B. Quental, Felipe G. Grazziotin, Michael L. Alfaro, Marcio Martins, Mericien Venzon, Hussam Zaher 2016
Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates
Molecular Phylogenetics and Evolution 105: 50–62

Carrasco, P.A., C.I. Mattoni, G.C. Leynaud, and G.J. Scrocchi. 2012
Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae).
Zoologica Scripta 41:1–15

[7] Crocodiles: Willis 2009 used an intron sequence to show a separate clade that includes Melanosuchus, Caiman, and Paleosuchus and may be called the Caimanidae:

Willis, Ray E. 2009
Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships.
Molecular Phylogenetics and Evolution 53 (3): 1049-1054

Man et al. (2011) suggested to divide the crocodiles into 2 families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma).

Man, Zhang; Wang Yishu, Yan Peng & Wu Xiaobing 2011
Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae.
Molecular Phylogenetics and Evolution 60: 62–67, doi:10.1016/j.ympev.2011.03.029.

For further taxonomic references on higher taxa see family pages or follow links to phylogeny pages.

This page is maintained by Peter Uetz

Created: 10 Nov 1995 / Last changed or updated: 21 Sep 2023