This study provides the first record of the two distinct mitochondrial lineages of Sinanodonta mussels in the Yenisei River that forms the largest Siberian river basin. It is the first discovery of alien populations of these mussels in Russia. The two mussel lineages are living in sympatry in a river site heated by warm water discharge of the Krasnoyarsk thermal power plant. These lineages represent two cryptic species: Sinanodonta aff. woodiana lineage E and S. ovata Bogatov and Starobogatov, 1996. The population of the first species from the Yenisei shares the invasive haplotype that is widely spread across Europe. The molecular evidence suggests that this lineage originated from the Yangtze River, China. The native distribution of the second species ranges across South Korea, Japan and small basins in the south of Primorsky Krai, Russian Far East. The possible vector of this invasion is the introduction of fish hosts or adult mussels by aquarists. Our results highlight that the populations of Sinanodonta species outside their native ranges may represent an overlooked but important threat for freshwater ecosystems in Russia that should be considered an unexpected nation-level ecological problem. Additionally, our discovery reveals the possibility of a successful joint invasion of different Sinanodonta species into a single river that may increase negative impacts of invaders on indigenous communities. Some implications of our findings for systematics of the unionid mussels are also discussed.