Amphisbaenians are a poorly known group of squamate reptiles with over 150 extant species in 23 genera. They live almost exclusively under loose or sandy soil in tropical to temperate areas around the world, and their anatomy is modified in many ways related to this lifestyle. Most recent studies recognize four families within Amphisbaenia—Bipedidae, Amphisbaenidae, Trogonophidae, and Rhineuridae. Only the Rhineuridae are well represented in the fossil record. Two exclusively fossil families, Hyporhinidae and Crythiosauridae, have also been recognized in some studies. In this paper, a phylogenetic study of the Amphisbaenia is presented based on morphological characters investigated in living and fossil forms. Amphisbaenian monophyly is supported, but the recent identification of the late Cretaceous Sineoamphisbaena hextabularis† as a primitive amphisbaenian is not supported. The monophyly of two of the four families of extant amphisbaenians is upheld, with one family being more inclusive than previously thought. Amphisbaenidae is substantially revised, with several taxa previously included in the family being more closely related to rhineurids, and with Blanus representing a basal amphisbaenian. Rhineuridae is also revised to include the previously recognized fossil family Hyporhinidae. Trogonophidae is the sister-group to the remaining amphisbaenids, and together they form the sister-group to the expanded rhineurid clade. Bipes is the most basal amphisbaenian and Blanus is the sister-group to all remaining amphisbaenians. Crythiosauridae is removed from the Amphisbaenia because no support was found for its inclusion.

The deep nesting of rhineurids within Amphisbaenia found here contrasts with their extensive fossil record beginning in the late Paleocene. This hypothesis implies significant gaps in the fossil record of all other amphisbaenian taxa, and the reacquisition of some seemingly primitive features in some fossil rhineurids. However, the condition of the limbs in extinct rhineurids is uncertain and, if they are found to be present, the related characters could place them in a more basal position, which would then alter interpretations of character evolution. The basal positions of Bipes and Blanus imply that a round-headed cranial shape is the primitive condition for Amphisbaenia in contrast to some previous hypotheses.

In this analysis, amphisbaenians are nested within Squamata, in contrast to a hypothesized relationship as the sister-group to the remainder of squamates (alone, with snakes, or with another group of limbless burrowing lizards, Dibamidae). Weak support was found for a relationship between amphisbaenians and Dibamidae as previously suggested by some other analyses, but this is based mainly on reduction and absence features and the sister-group to Amphisbaenia is considered here to be inconclusive. Sineoamphisbaena† is found to be related to macrocephalosaurs, an extinct group previously placed with Teiidae, but placed basally among squamates by this analysis.

Morphological analyses of squamates in this study include numerous features associated with reduced or absent limbs and limb girdles, as well as other specializations presumed to be related to a burrowing lifestyle. These characters are often hypothesized to have been convergently acquired among limbless squamate clades and have been excluded or downweighted in some previous analyses. This approach is difficult to implement here because further anatomical investigations of these structures revealed useful variation for resolving relationships within amphisbaenians. Future studies will require new approaches that can address the c