Microsatellite markers were tested to rapidly discriminate five Japanese genotypes (US-1, JP-1, JP-2, JP-3, and JP-4) of Phytophthora infestans. Collected from 1958 to 2007, 111 isolates of Japanese P. infestans were examined using a fluorescent-labeled primer and capillary electrophoresis. Microsatellite marker Pi26 generated specific products for each genotype without any differences in terms of isolation area or year for a particular genotype. The Pi26 marker is a powerful tool for obtaining information on the structure of Japanese populations of P. infestans.