Cat-eyed snakes (Leptodeira) were thought to be closely related to nightsnakes (Hypsiglena and Pseudoleptodeira) based on morphology and immunological data, which allied these genera with blunt-headed vine snakes (Imantodes) and the Cloud Forest Snake (Cryophis hallbergi ). We collected sequence data from six protein-encoding nuclear loci (SLC30A1, ZEB2, FSHR, NTF3, DNAH3, and PNN; 4149 bp) and additional mtDNA data (nad5; 955 bp) added to published cob and nad4 (total 2387 bp mtDNA) from these and other rear-fanged, mildly venomous snakes that prey on vertebrates (frogs and lizards) and from several other dipsadine genera (Dipsas, Sibon, and Atractus) that prey on invertebrates (goo-eaters). We analyzed relationships using concatenation and a coalescent species-tree method. When analyzed separately, using either concatenation or coalescent methods, nuclear data support a different overall topology from the mtDNA data. Like the mtDNA data, the nuclear data support the Leptodeira + Imantodes relationship, but instead place this clade more closely to the goo-eaters, with the nightsnakes as the basal divergence in the group. When the data are combined in concatenation analyses, the more variable mtDNA data appear to overwhelm the nuclear data, but not under the coalescent model.