Sponges in the large rivers within the Danube River Basin (DRB) have not been adequately studied. Hence, the aim of this work was to undertake an investigation on the distribution of sponge species in the Danube and Sava rivers. Out of 88 localities covered by the study, sponges were found at 25 sites only (46 samples in total). By using morphological (light and scanning electron microscopy) and genetic (28S rDNA sequencing) analysis, four species were determined: Ephydatia fluviatilis (Linnaeus, 1759), Spongilla lacustris (Linnaeus, 1759), Eunapius fragilis (Leidy, 1851), Trochospongilla horrida Weltner, 1893. In the Danube, the predominant species was found to be E. fluviatilis making approximately 80% of collected samples, while in the Sava River S. lacustris dominated, representing 46% of the river sponges. Our work represents one of the few studies on freshwater sponges within the DRB from long stretches of the large lowland rivers (more than 2500 km of the Danube River and about 900 km of the Sava River). Moreover, molecular analysis for the identification of freshwater sponges was applied on the material collected from a wide area, thus contributing to the systematic studies on the distribution and abundance of the European freshwater invertebrate fauna in general.