The threatened Bluetail Mole Skink (Plestiodon egregius lividus) is limited to the xeric habitats of the southern Lake Wales Ridge in central Florida. To generate important data for conserving this species, we characterized genetic variation at the mitochondrial cytochrome-b gene and seven microsatellite loci among multiple populations. We compared the Bluetail Mole Skink's pattern of genetic diversity and differentiation to those of two other lizards with similar geographic and habitat distributions—the Florida Sand Skink (Plestiodon reynoldsi) and the Florida Scrub Lizard (Sceloporus woodi). The Bluetail Mole Skink was highly variable at the genetic markers, and significant genetic differentiation occurred among scrub patches. Patches can be divided into central and southern Lake Wales Ridge groups. Our results also suggest that each sampled habitat patch should be treated as a population and reintroductions should minimize the distance between recipient and source locations to limit altering the potential long-term pattern of genetic differentiation among Bluetail Mole Skinks on the Lake Wales Ridge. The Bluetail Mole Skink and the Florida Sand Skink had similar genetic diversity, and all three lizards had comparable patterns of genetic differentiation. The concordance of genetic differentiation among these species is further evidence suggesting that similar conservation issues face the three species, namely, preserving the remaining xeric habitat. It is likely, therefore, that conservation efforts directed at the more common Florida Sand Skink and Florida Scrub Lizard would benefit the Bluetail Mole Skink.