Most fisheries involving spiny lobsters of the genus Palinurus have been overexploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.650 ± 0.077 SD (Palinurus barbarae) to 0.792 ± 0.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower water species consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity.