ABSTRACT Plasmopara viticola populations collected from three islands in the Ionian Sea-an arm of the Mediterranean Sea to the west of Greece-were analyzed with microsatellite molecular markers in order to investigate the pathogen population structure. Downy mildew populations from mainland regions previously studied were found to have high genotypic diversity and limited clonality; however, populations under Mediterranean island conditions mostly showed limited variation and the epidemics basically were driven by the multiple clonal infections of one or a few genotypes. Populations from different islands were differentiated from each other, whereas genetic divergence also was found among subpopulations of the same plot. Polyploid individuals and individuals that overwintered in asexual form were observed in some cases. The findings obtained by this population genetics study improve our understanding of the biology of the pathogen and lead to potential alternative control measures for the disease.