The first molecular phylogeny is presented for four species of the scorpion genus Mesobuthus, based on DNA sequences of three gene fragments (two mitochondrial and one nuclear protein coding gene, ∼1 kb). The inferred phylogeny based on a pooled maximum likelihood analysis revealed a clear deep splitting between the “western clade” consisting of M. gibbosus and M. cyprius (Greece/Anatolia, Cyprus) and the “eastern clade” consisting of M. eupeus and M. caucasicus (Anatolia/Central Asia). The species M. caucasicus (recently placed in the genus Olivierus Farzanpay 1987) groups monophyletically within Mesobuthus; thus, the genus Olivierus is synonymized here with Mesobuthus. Sequences of M. eupeus and M. caucasicus sampled mainly from Kazakhstan and Uzbekistan are highly structured, indicating the possible existence of multiple species.