Unresolved phylogenetic relationships within the subfamily Natricinae continue to exist, including the position of the genus Xenochrophis. In the present study, two mitochondrial genes (cytochrome b, 12S rRNA) and one nuclear gene (c-mos) were used to infer the phylogenetic relationships among the members of Natricinae, with a special emphasis on the position of the genus Xenochrophis. Two statistical methods, Maximum Likelihood and Bayesian Inference, were used for phylogenetic reconstruction. Both the mitochondrial and nuclear datasets produced sufficiently resolved and congruent topologies. Our findings placed the genus Xenochrophis within Natricinae consistently with strong nodal support. Findings also revealed a close association between two Indian natricid snakes, Xenochrophis piscator and Xenochrophis schnurrenbergeri. However Xenochrophis vittatus, from Indonesia, does not cluster with the remaining species of Xenochrophis, suggesting a nonmonophyly of this genus. Overall Natricinae was found to be monophyletic because the two genera, Psammodynastes pulverulentus and Amplorhinus multimaculatus, are now known to be members of the Lamprophiidae. This study also finds a close relationship between the endemic species Lycognathophis seychellensis with the African natricids.