Maintaining a meta-population structure significantly contributes to species viability and is often the basis for defining the difference between a naturally patchy and a fragmented landscape. However, a heterogeneous landscape may be patchy for habitat generalists and fragmented for specialists, preventing the formation of meta-population structures in habitat specialists. We examined this hypothesis on the generalist Lichtenstein's short-fingered gecko Stenodactylus sthenodactylus and the endangered specialist Middle Eastern short-fingered gecko S. doriae, two species of the genus Stenodactylus, inhabiting the southern Arava Valley in Israel. We compared the genetic structure of the populations of these two geckos by amplified fragment length polymorphism analysis, expecting to find decreased gene diversity within the small populations that fail to form a meta-population structure. Indeed, we found that among populations, the habitat specialist S. doriae had a low level of gene flow, whereas the habitat generalist S. sthenodactylus had a relatively high level of gene flow. However, unexpectedly, the most isolated population of the specialist S. doriae, located in the Samar dune (a small patch of 2.3 km2), exhibited the highest level of gene diversity of all the populations studied (expected heterozygosity = 0.4286). Moreover, the results showed that the Samar population is genetically unique when compared with its neighboring populations. Gene flow between two populations located to the north and to the south bypass the Samar population. The generalist S. sthenodactylus, in contrast, did not exhibit an exceptional level of gene diversity. The origin of the exceptional diversity and genetic uniqueness of the Samar population of S. doriae may be associated with traits that make this gecko highly adaptive to this specific landscape unit. It also emphasizes the need to establish special conservation efforts for the protection of high-quality habitats that provide adequate conditions for a source population of specialist species.