Freshwater mussels are an endangered group of animals, especially in the water bodies of Central and Western Europe. Conservation priorities were established for many endangered freshwater mussel species in the last decade. Here, we present new data on a cryptic refugium of freshwater mussels in the Western Balkans. Two species, Anodonta exulcerata Porro, 1838 and Unio elongatulus Pfeiffer, 1825, were discovered in Montenegro for the first time. The phylogenetic position and taxonomic status of freshwater mussel species from Montenegro were studied by means of an integrative approach, combining morphological data and COI gene sequences. Unio carneus Küster, 1854 stat. rev. represents a species with a restricted range, which is endemic to the Western Balkans. A viable population of Microcondylaea bonellii (Férussac, 1827) was discovered in the Zeta River. This species was not mentioned in Montenegro since the 1900s. A significant level of genetic diversity was revealed for the studied species. In the Skadar Lake basin, freshwater mussels from diverse ecological groups were discovered. Rheophilic species of freshwater mussels may represent ancient lineages, which need special conservation planning. Conservation priorities should be aimed at the protection of freshwater mussel habitats on the Balkan Peninsula.