Maximum likelihood (ML) and Bayesian inference (BI) analyses of the complete nucleotide sequences of the cytochrome b gene (cytb) were used to examine the phylogenetic position of the rare snake Xenophidionschaeferi within the alethinophidian snakes. The cytochrome b sequence of this representative of the poorly known family Xenophiidae was compared with those of a large and comprehensive suite of alethinophidian taxa. The research presented here represents the first time all families of alethinophidian and caenophidian snakes have been included in a single molecular phylogenetic study. Results from ML and BI analyses suggest a possible sister taxon relationship between Xenophidion schaeferi and the Bolyeridae. Moreover, strong statistical support also indicates that Xenophiidae is a member of a clade that contains Pythonidae, Loxocemidae, Uropeltidae, Xenopeltidae and Bolyeriidae. Additionally, maximum parsimony and BI analyses of previously published morphological data revealed that these anatomical character states and potentially low taxonomic sampling produced little phylogenetic information valuable to understanding the relationship of Xenophiidae among the Alethinophidia.