||Bavayia crassicollis is a coastal gecko species currently understood to inhabit the southern and eastern islands of New Caledonia in the southern Pacific Ocean. This distribution is unusually large and disjunct for this genus. To test the monophyly of this group and to examine the nature of the relationship between geographic distribution of these populations and their genetic structuring, Bavayia crassicollis populations were sampled and analyzed using mtDNA sequencing and Amplified Fragment Length Polymorphisms (AFLP). MtDNA analyses suggest that the populations from the Isle of Pines (IDP) area are a monophyletic group more closely allied with Bavayia robusta rather than the type locality of crassicollis in the Loyalty Islands. These analyses also suggest hybridization events have occurred from both robusta and crassicollis to the IDP clade. These results modify the known distribution of Bavayia geckos and, pending additional AFLP data, support the elevation of IDP populations to species status.