In this paper, three historical biodiversity datasets (from 1940s, 1980–1999 and 2000–2004) and results from the recent inventory are used to trace the long-term changes of the mollusks in the eutrophic Lake Dianchi. Comparison of the obtained results with those of earlier investigations performed during the period of 1940s and 1980–1999 as well as 2000–2004 showed that changes have occurred in the interval. There were 31 species and 2 sub-species recorded prior to the 1940s, but the species richness decreased from a high level of 83 species and 7 sub-species to 16 species and one sub-species from 1990s to the early of 21st century in lake body. Species from the genera of Kunmingia, Fenouilia, Paraprygula, Erhaia, Assiminea, Galba, Rhombuniopsis, Unionea and Aforpareysia were not found in Dianchi basin after 2000. The species from the genera Lithoglyphopsis, Tricula, Bithynia, Semisulcospira and Corbicula were only found in the springs and upstream rivers. Anoxia and the changing of substrates and fish species composition could explain why molluscan community composition changed in eutrophic Lake Dianchi. Additionally, the different sampling methods and ignore of the specific groups in earlier studies are cause for Sphaerium and Pisidium first found in our study. This study is first time to enlarge the investigation region to the Dianchi basin. Although some endemic species disappeared in the lake body, they still distribute in the springs and upstream rivers. The springs and upstream rivers are important refuges for mollusks.