This database does not provide detailed accounts for higher taxa. However, for each group we link to pages on Wikipedia, indicated by a W. The family links will list all species within that family.
Note that a hierarchical system as shown here does not reflect the actual relationships among reptiles. Also, there are additional clades that are not shown here, e.g. birds (a sbuset of archosaurs) and fossil clades. Take a look at the phylogenetic overview here or at the phylogeny pages linked below for more information.
- Family Emydidae (Pond Turtles/Box and Water Turtles) W
- Family Testudinidae (Tortoises) W
- Family Geoemydidae (Bataguridae) (Asian River Turtles, Leaf and Roofed Turtles, Asian Box Turtles) W
- Family Platysternidae (Big-headed Turtles) W
Suborder Pleurodira (phylogeny)
Order Squamata (phylogeny of squamata) 
Sauria (Lacertilia) - Lizards
Infraorder Iguania 
- Family Agamidae (Agamas), incl. Leiolepididae W
- Family Chamaeleonidae (Chameleons) W
- Superfamily Iguanidae s.l. ("Iguanas") [Pleurodonta]
- Family Corytophanidae (Casquehead Lizards) W
- Family Crotaphytidae (Collared and Leopard Lizards) W
- Family Dactyloidae (Anoles s. str.)
- Family Hoplocercidae (Wood lizards, Clubtails) W
- Family Iguanidae s. str. (Iguanas and Spinytail Iguanas) W
- Family Leiocephalidae
- Family Leiosauridae
- Family Liolaemidae
- Family Opluridae (Madagascar iguanids) W
- Family Phrynosomatidae (Earless, Spiny, Tree, Side-blotched and Horned Lizards) W
- Family Polychrotidae (Anoles) W
- Family Tropiduridae (Neotropical Ground Lizards) W
- Family Gekkonidae (Geckoes) W
- Family Carphodactylidae
- Family Diplodactylidae W
- Family Eublepharidae W
- Family Phyllodactylidae
- Family Sphaerodactylidae
- Family Pygopodidae (Legless Lizards) W
Infraorder Scincomorpha 
- Family Cordylidae (Spinytail Lizards) W
- Family Gerrhosauridae (Plated Lizards) W
- Family Lacertidae (Lacertids, Wall Lizards) W
- Family Scincidae (Skinks) W -- see below and note in News
- Subfamily Acontinae (Limbless skinks)
- Subfamily Egerniinae (Social skinks)
- Subfamily Eugongylinae (Eugongylid skinks)
- Subfamily Lygosominae (Lygosomid skinks)
- Subfamily Mabuyinae (Mabuyid skinks)
- Subfamily Sphenomorphinae (Sphenomorphid skinks)
- Subfamily Scincinae (Typical skinks)
- (Sub-) family Ateuchosauridae (East Asian skinks) -- not currently recognized
- (Sub-) family Ristellidae (Indo-Sri Lanka skinks) -- not currently recognized
- Family Xantusiidae (Night Lizards) W
Superfamily Gymnophthalmoidea (after Goicoechea et al. 2016) (new!)
- Family Alopoglossidae
- Family Gymnophthalmidae (Spectacled Lizards) W
- Family Teiidae (Whiptails and Tegus) W
Infraorder Diploglossa (note 1)
- Family Anguidae (Glass Lizards and Alligator Lizards; Lateral Fold Lizards) W
- Family Diploglossidae (Galliwasps and South American Glass Lizards)
- Family Anniellidae (American Legless lizards) W
- Family Xenosauridae (Knob-scaled Lizards) W
Infraorder Platynota (Varanoidea) (note 1)
- Family Helodermatidae (Gila Monsters) W
- Family Lanthanotidae (Earless Monitor lizards) W
- Family Varanidae (Monitor Lizards) W
- Family Shinisauridae
Amphisbaenia (revised after Vidal & Hedges 2009)
Ophidia (Serpentes) - Snakes (phylogeny) 
Superfamily Uropeltoidea s.l. (Pipe snakes and Shield-tailed snakes)
- Family Anomochilidae (Dwarf Pipe Snakes) W
- Family Cylindrophiidae (Asian Pipe Snakes) W
- Family Uropeltidae (Shield-tail Snakes) W
Superfamily Pythonoidea s.l. (Pythons and relatives)
- Family Loxocemidae (Mexican Burrowing Pythons) W
- Family Pythonidae (Pythons) W
- Family Xenopeltidae (Sunbeam Snakes) W
Superfamily Booidea (preliminarily after Vidal & Hedges 2009)
- Family Boidae (Boas) W
Superfamily Colubroidea (revised after Pyron et al. 2010, Pyron et al. 2013)
- Family Colubridae (Colubrids) W
- Family Dipsadidae W (Dipsadinae in Pyron et al. 2013)
- Family Lamprophiidae (in Wikipedia currently subsumed under Colubridae)
- Family Natricidae W (Natricinae in Pyron et al. 2013)
- Family Pseudoxenodontidae (Pseudoxenodontinae in Pyron et al. 2013)
- Family Elapidae W (for the superfamily Elapoidea see note )
- Subfamily Elapinae (Cobras, Coral Snakes, etc.)
- Subfamily Hydrophiinae (Sea Snakes)
- Family Homalopsidae W
- Family Pareatidae W
- Family Viperidae (Vipers and Pit Vipers) W
- Family Xenodermatidae
Superfamily Typhlopoidea (Scolecophidia)
- Family Anomalepididae (Dawn Blind Snakes) W
- Family Gerrhopilidae (Blind Snakes)
- Family Typhlopidae (Blind Snakes) W
- Family Leptotyphlopidae/Glauconiidae (Slender Blind Snakes) W
- Family Xenotyphlopidae
Currently not assigned to any Superfamily:
Order Crocodylia - Crocodiles etc. 
Overall taxonomy originally after
Vitt, Laurie J.; Janalee P. Caldwell 2013
Herpetology, Fourth Edition: An Introductory Biology of Amphibians.
Academic Press, 776 pp. [ISBN 978-0123869197] 
 Turtles mainly after
For more recent analyses see
Krenz, James G.; Gavin J.P. Naylor; H. Bradley Shaffer and Fredric J. Janzen (2005) Molecular phylogenetics and evolution of turtles.
Molecular Phylogenetics and Evolution, Volume 37 (1):178-191
Crawford, N.G. et al. (2014) A phylogenomic analysis of turtles. Molecular Phylogenetics and Evolution. Crawford et al. erected a number of higher taxa, e.g. the group Trionychia for the Carettochelyidae and Trionychidae. However, they did not precisely define which genera are in each group (as theyr phylogeny contains only a third or so of all turtle genera), hence we do not use them in the database yet.
 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
 Iguania after
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.
However, a morphological analysis of the vaginal-cloacal region still yields a different topology, e.g. with the Dibamidae, Xantusiidae, and Amphisbaenia forming one branch:
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
 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.).
 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
PHYLOGENY, BIOGEOGRAPHY AND CLASSIFICATION OF THE SNAKE SUPERFAMILY ELAPOIDEA: A RAPID RADIATION IN THE LATE EOCENE.
Cladistics 25: 38-63
 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.