The duck mussel Anodonta anatina is widely distributed throughout the freshwater basins of Northern, Central, and Western Eurasia, and it has a comprehensive genetic structure. This study was devoted to the analysis of lineages, which are defined based on COI gene sequences. Our new dataset was expanded by samples from freshwater basins of Northern and Central Eurasia. It allowed us to reveal a high level of genetic diversity for the widely distributed trans-Eurasian lineage of A. anatina for the first time. As for results, representative samples from the Russian Plain, Southern Siberia, and the Ural region showed the presence of multiple interactions between duck mussel populations, indicating the existence of connections between freshwater basins in this region during the Late Quaternary. The genetic group from the freshwater basins of Northern Eurasia may be divided into two sub-lineages, which have differences in genetic structure and distribution patterns. It was revealed that there was a post-glacial expansion of duck mussels in the freshwater basins of Northern Eurasia after deglaciations of these territories and that the wide distribution of this species in this region was shaped via ancient connections between periglacial waterbodies. The lineage of A. anatina from the Ponto-Caspian region is a genetically rich and diverged group, which is present in the riverine basins of West-Central Asia related to the Caspian Sea.