The head of Anomochilus weberi combines features seen in living uropeltines and scolecophidians, two clades of fossorial snakes that appear to have the most specialized and, at the same time, the most divergent modifications of the head. However, the weakly supported premaxilla of Anomochilus departs from both scolecophidian and uropeltine modes of reinforcing the anterior tip of the snout, suggesting that Anomochilus is a less specialized burrower. Its skull also has a number of features unusual among snakes, including a unique buttress on the anterior ends of the septomaxillae, an ectopterygoid reduced to a splint that touches neither maxilla nor pterygoid, a short maxillary tooth row oriented a t 45" to the long axis of the skull, and a braincase and snout complex that are uniformly wide. The features of the upper jaw are predicted to confer behavioural and mechanical attributes intermediate between those of typhlopid scolecophidians and uropeltines.

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Phylogenetic analysis of 38 skeletal characters, 12 muscular characters and 15 visceral characters in 17 major snake clades plus Anomochilus suggests that Anomochilus is the sister taxon of all other living alethinophidian snakes. However, skeletal, muscular and visceral character sets analysed separately or in pairs give four groups of nonconcordant tree topologies. Based on the cladogram derived from the total evidence, two families are erected to prevent the existing family Uropeltidae from becoming paraphyletic: Anomochilidae, for the Malaysian and Indonesian genus Anomochilus, and Cylindrophiidae, for the Sri Lankan, Southeast Asian and Indonesian genus Cylindrophis and the Upper Eocene fossil Eoanilius.