Switzerland’s drainage systems are divided into three major European river basins, i.e. the Po, the Rhône, and the Rhine basins. Until recently 32 species of freshwater mussel species (i.e. belonging to the genera Anodonta and Unio) were recognized for the country, albeit their identity and number remain uncertain especially, given the recent recognition of Unio mancus Lamarck, 1819 from the Rhône in France, and Unio elongatulus C. Pfeiffer, 1825 and Anodonta exulcerata Porro, 1838 from the Po basin in Italy. In this study, we molecularly assess Swiss populations of freshwater mussels to understand the identity and number of species as well as to characterize their distributions within this geologically differentiated Alpine country. We collected 125 specimens in 42 lakes and rivers representing the three major basins and performed a phylogenetic investigation of the collected specimens using two mitochondrial markers (COI & 16S) and one nuclear marker (28S). COI Haplotype networks are then presented for the identified species. Our new findings show that Unio elongatulus inhabits water bodies north of the main Alpine arc. No living populations of Unio mancus could be detected in Switzerland. Anodonta exulcerata is recorded from two localities north of Lake Maggiore and in the Swiss part of Lake Lugano. Anodonta anatina (Linnaeus, 1758) shows genetic differences between southern alpine and northern alpine populations. Our genetic data from Swiss populations of unionid species provides new records and knowledge concerning freshwater mussels from Central Europe and specifically from the Alpine region.