In recent studies nine populations of the freshwater pearl mussel have been described in the Baltic Sea basin in Russia. They are very scarce, although the condition of their habitats seems to be rather good. Overfishing of the host fish is a limiting factor for them. The number of salmon has decreased by at least 100 times over the past 200 years. Such a scale of decline tends to be hidden over time, and estimation of the normal conditions of the salmon–pearl mussel ecosystem becomes problematic. A significant increase in the number of salmon is necessary to prevent extinction of pearl mussels. Effective protected areas appear to be the only possibility for conservation of the pearl mussels and its host fish species.