ABSTRACT: Posidonia oceanica is an endemic seagrass species in the Mediterranean Sea. Due to its ecological importance, it has been the subject of several genetic studies aimed at increasing general knowledge of the system and helping to define appropriate management strategies. We compared the efficiency of 2 different classes of molecular markers, ‘inter simple sequence repeats’ (ISSRs) and ‘simple sequence repeats’ (SSRs) or ‘microsatellites’, in population genetic analysis of P. oceanica. To do this, we analyzed meadows along the coasts of the Calabria peninsula (Italy, South Tyrrhenian Sea and Ionian Sea), a putative biogeographic barrier for P. oceanica. SSR and ISSR markers detected different levels of genetic variability within P. oceanica populations. Dinucleotide microsatellites were more polymorphic than tri- and heptanucleotide microsatellites and ISSRs. Nevertheless, discriminating power analysis performed for each single locus showed that some trinucleotide microsatellite and ISSR primers were more sensitive than dinucleotides. The use of selected ISSR and SSR markers together allowed the detection of higher polymorphism than either set of marker alone. Tyrrhenian meadows were always more polymorphic than Ionian ones, according to both SSRs and ISSRs. Both markers strongly suggested the Calabria peninsula as an important biogeographic barrier between the Western and the Eastern side of the Mediterranean basin.