Freshwater pearl mussels (family Margaritiferidae) are sensitive to human impact and environmental changes. Large declines in their abundance have prompted studies of distribution and estimations of population densities. Iturup Island, a part of Kuril Islands, Russia, is considered to be within the distribution area of freshwater pearl mussels, but this information is based on only two specimens collected several decades ago. Detailed survey of the island is challenging as most of its territory is nearly impassable. A preliminary analysis of island rivers was carried out prior to the surveys to discover potential freshwater pearl mussel habitats. Based on previous experience from European Russia, freshwater pearl mussel habitat was expected to occur in rivers flowing out of lowland lakes. Live individuals of Margaritifera laevis were found during surveys in one river together with the unionid Beringiana beringiana, which were also found in two other rivers where the predicted habitat occurred. Based on prediction and surveys, the occurrence of freshwater pearl mussels in other rivers of Iturup Island is unlikely. Pearl mussels were concentrated in a small section of the Zmeika River with a population of about 100,000 mussels. Present threats to the population include overharvest of host fish masou salmon (Oncorhynchus masou). Surveys using similar methods can help to reveal unknown freshwater mussel populations on other Kuril Islands and on the mainland.