A wide bivalve mollusc variety is infected by Perkinsus mediterraneus in Balearic Islands: Ostrea edulis, Mimachlamys varia, Arca noae, Chamelea gallina, Pinna nobilis and Venus verrucosa. Perkinsus spp. search was performed using RFTM and species was established by PCR-RFLP and sequencing. We have found 12 P. mediterraneus haplotypes, all of them sharing a high similarity. Three groups of O. edulis from Minorca were revealed by phylogenetic analyses which are different from other co-specifics lineages. Analysis supported this differentiation among populations from Minorca and Majorca. This differentiation could be due to Mahon harbour geographic isolation. Nevertheless, other factors, such as environmental variability, different detection locations and dates, animal translocations, human activity, etc., might also have some influence. Although it is known that co-infections between P. olseni and P. mediterraneus can happen in Venus verrucosa from Mahon harbour, we have not found any occurrence. Furthermore, we have not detected infection by P. chesapeaki, although it has been found in the Ebro delta. This work establishes distribution, affected species, their genetic variability, its prevalence and the infection dynamics by P. mediterraneus.