Recent work revealed surprisingly deep mitochondrial genetic divergence in the lizard Anolis cristatellus among samples obtained from the small Caribbean island of Vieques. We sought to determine whether this had resulted from natural or anthropogenic causes, and (if the former), whether divergence occurred in a biogeographic context of allopatry followed by secondary contact, or via isolation-by-distance across the species’ historical range. We first estimated a mitochondrial gene tree for 379 samples and then genotyped 3,407 single nucleotide polymorphic sites from 48 individuals using a modified genotyping-by-sequencing approach. We found that Anolis cristatellus samples from Vieques belong to two highly divergent mitochondrial subclades, but the geographic distribution of these haplogroups indicates that this pattern is most-likely natural in origin. Analysis of our SNP dataset revealed differentiation that is consistent with isolation-by-distance between the western and eastern ends of Vieques, suggesting that the overall pattern of divergence likely reflects primary intergradation with a mitochondrial break on the historical Puerto Rico Bank paleo-island that happened to coincide with the present-day island of Vieques. Our findings help underscore the growing consensus that results from a single genetic marker can prove highly misleading in studies of historical population genetic structure.