The freshwater pearl mussel Margaritifera margaritifera (L., 1758) is considered to be a critically endangered species. It is important to obtain information on the distribution and status of the surviving populations of the species, but in Russia this work is still problematic due to the size of the country's territory, combined with the insufficient number of available specialists. “Searching rules” have been proposed to remotely identify potential pearl mussel habitats in rivers. The most important criteria are relating to the lakes found at the rivers’ sources, as well as to the extent of the deforestation along river basins. About 200 watercourses of the Russian section of the Baltic Sea basin were evaluated using these “rules”. As a result, two previously unknown, viable populations were discovered (comprising about 53,000 specimens), while the absence of pearl mussels was made evident among some rivers which were traditionally believed to be their habitats. The obtained data provides an update on the status of pearl mussels in Russian territories located south of the 61 st degree of latitude. There are 10 populations of this species; 4 of them are almost extinct, 6 are relatively numerous but declining. The total number of pearl mussels hardly exceeds 90,000 individuals.