Cyclura carinata, a critically endangered Caribbean rock iguana, now occupies less than 5% of its historic range. Remaining populations are genetically structured, but available tools are insufficient to identify taxonomic units. Ten polymorphic microsatellites isolated from C. carinata, and 19 loci developed for congeners are identified. All 29 loci were screened for variation in two populations with 20 or more individuals from each of two island populations, as well as 24 individuals that are representative of the species range.