This paper presents results of a malacological survey of the middle and upper section of the Jihlava River, a tributary of the Dyje River (Czech Republic). Twenty-three species of aquatic molluscs (13 gastropods, 10 bivalves) were found at 35 sites during research realised mostly in 2017 and 2020. In comparison with the lower section of the Jihlava River, a significantly lower proportion of bivalves of the family Unionidae was found in the middle and upper sections.