Skeletonema potamos is a freshwater diatom that has been widely distributed in North America, Europe, and Australia since the 1980s. However, there have been few previous reports of S. potamos in China. Only recently has S. potamos been frequently found in our extensive ecological surveys in China, and it has sometimes even been the dominant species. This study clarified the morphology, distribution, and origin of S. potamos, as well as the underlying mechanism contributing to its dominance. We examined the samples collected from the Changjiang River (Yangtze River) Basin during 2016–2022 and determined their geographical distribution. Genetic distance analysis indicated that S. potamos strains in China might have been transported by ships and ballast water from the USA or Japan through the East Sea into the Yangtze River Estuary. Cargo ships possibly contribute to its dispersal. An analysis of the ecological factors affecting the occurrence and distribution of S. potamos in China indicated that many waterbodies provide environments suitable for S. potamos. The suitable environment, small size, and rapid reproduction of S. potamos are the reasons for its dominance in the Yangtze River Basin. We predict that S. potamos is likely to form “blooms” in China in the future.