Abstract Scorpions of the genus Mesobuthus represent a useful terrestrial model system for studying molecular evolution. They are distributed on several Aegean islands and the adjacent mainland, they are believed to have low rates of dispersal, and evolutionary divergence dates of taxa are available based on biogeographic events that separated islands from each other and the mainland. Here, we present data on polymorphism and synonymous (K2) and nonsynonymous (K2) substitution rates for nine nuclear protein-coding genes of two east Mediterranean scorpion species, Mesobuthus gibbosus and M. cyprius (Buthidae). Levels of polymorphism tend to be lower in populations from islands (mean nucleotide diversity π 5 0.0071 |pL 0.0028) than in mainland populations (mean ±= 0.0201 ± 0.0085). By using linear regression of genetic divergence versus isolation time, we estimate K2 to be 3.17 ± 1.54 per (site × 109 years), and K2/sb> to be 0.39 ± 0.94 per (site × 109 years). These estimates for both K2 and K2 are considerably lower than for many other invertebrates, such as Drosophila, and may be attributed to scorpions' mammal-like generation times (∼2 years) and low metabolic rates. Phylogenetic analysis using maximum likelihood revealed a phylogeny that is congruent with that expected based on biogeographic events and in which divergences at synonymous sites are proportional to the dates that the taxa are believed to have split. Tests of equality of branch lengths for the Cyprus and Crete lineages revealed that Ks-estimates are about the same in both lineages, as expected from the biogeographic events that separated the islands, but Ka was increased in the Cyprus lineage compared to the Cretan lineage.