ABSTRACTThe two highly endangered European mussel species Margaritifera margaritifera and Unio crassus are target species of conservation. Based on a recently completed systematic state‐wide monitoring of each 22 M. margaritifera and 22 U. crassus streams in Bavaria, Germany, we present an update on population trends, conservation status, habitat quality and threats for both species. Populations status and habitat quality varied strongly between M. margaritifera and U. crassus streams, but there was also great variability within each of those groups. The population decline of M. margaritifera has continued, albeit higher proportions of juveniles originating from artificial breeding programmes have been established in some streams. Habitat quality often did not match known requirements as evident from poor stream bed quality, lack of hosts and elevated nutrient levels. In contrast, U. crassus populations showed a better status, with an increase in population size over all sampled streams. Successful recruitment was indicated by high proportions of juveniles. However, no mussels older than 16 years were found, probably due to predation and structural stream maintenance measures. Climate change effects, such as extreme droughts, affected both species. This study demonstrates different needs in conservation management for both species. Although mitigation of drought effects is commonly needed for both species, tackling host fish management and direct threats such as predation should be prioritized in U. crassus, whereas restoration of prime habitat quality and intact catchments is key to enable natural recruitment and sustainable populations of M. margaritifera.