The Gyrodactylus spp. fauna on species of gobies, Pomatoschistus, Gobiusculus, and Knipowitschia (Gobiidae: Teleostei), from the western Mediterranean and Adriatic seas is strikingly similar to that found in the Baltic Sea and eastern Atlantic Ocean, both in morphology and in internal transcribed spacer (ITS) rRNA. The fauna consisted of Gyrodactylus branchialis, G. ostendicus, G. gondae, G. rugiensis, G. rugiensoides, and G. arcuatus. No new species have been found. A morphometric comparison between G. branchialis from the Mediterranean and Adriatic seas and its type locality in Ostend (Belgium) showed significant differences in ventral bar and marginal hook features. The morphometric variation was lower in G. rugiensis, whereas no significant differences were found in G. ostendicus. Gyrodactylus branchialis and G. ostendicus collected on P. microps were slightly different in the ITS rDNA (-0.6%) compared with specimens on the closely related P. marmoratus, probably reflecting ongoing speciation. A hybrid zone was identified in the Vaccarès lagoon complex (France) where both host species are sympatric. There was no clear geographic or host-related pattern in the variation found in the ITS2 rDNA in G. arcuatus sampled from P. microps, G. flavescens, Pungitius pungitius, K. panizzae, and its original host Gasterosteus aculeatus (2 polymorphic sites). Of all studied species, only G. arcuatus, G. rugiensis, and G. rugiensoides showed minor intraspecific variation in the ITS rDNA. Hence, the physical separation by a shoreline of more than 10,000 km is hardly reflected in the parasite ITS rDNA.