Two sedentary gobiids (the cryptic species Pomatoschistus microps and P. marmoratus) have been analysed in several Mediterranean lagoons of southern France and in Corsica. In order to determine the level of population isolation between neighbouring lagoons, mtDNA was screened using RFLP (7 endonucleases) of an amplified 2 kb region (including the D-loop and Cyt b). The mtDNA diversity of the genus is high (42 haplotypes for 125 individuals) so that a detailed haplotype tree has been constructed using two additional outgroup species. The main result is that almost no common haplotypes are shared between populations of the same species inhabiting neighbouring lagoons. A high level of isolation between neighbouring lagoons during several centuries is deduced, at least for P. microps populations.