The Homalopsinae (Oriental-Australian rear-fanged water snakes) is a small (34 species, 10 genera) colubrid subfamily notable for its ecological and morphological diversity. Despite considerable interest in the ecology and evolution of this group, phylogenetic relationships within the subfamily are poorly resolved. We present the results of a molecular phylogenetic study of the homalopsines based on partial sequence of three mitochondrial genes (12S and 16S ribosomal RNA and cytochrome b) from 14 ingroup species, five Old and New World natricines and the Old World colubrid, Dinodon semicarinatus. Maximum likelihood analysis in combination with bootstrapping and Bayesian Markov chain Monte Carlo methods for assessing phylogenetic confidence revealed that the single most likely topology contained a number of well-supported nodes. Homalopsine monophyly was strongly supported with respect to the outgroups included in our study. Cantoria violacea, a morphologically distinctive marine crustacean eater, formed the sister group to the rest of the homalopsines. Enhydris, the most species-rich genus in the subfamily, was polyphyletic with respect to other homalopsines although five morphologically and ecologically similar species formed a well-supported clade. The marine crustacean eaters Fordonia leucobalia and Gerarda prevostiana, also formed a novel clade. We discuss the evolutionary and ecological implications of this phylogeny for the Homalopsinae.