AbstractAimThe indirect consequences of biotic homogenization, the process of a gradual increase in the similarity of regional biotas driven by the combined effects of species invasions and extinctions, are still poorly understood. In this study, we aimed to assess the ability of a native affiliate species to maintain its host resources under the condition of biotic homogenization of host communities.LocationCentral (Vltava River Basin, Czech Republic) and western (Douro River Basin, Portugal) Europe.MethodsWe tested the ability of non‐native species to serve as an alternative partner in local host–affiliate relationships. We used a European freshwater mussel, Anodonta anatina, which is considered to be a host generalist of native fish species, and compared the compatibility of its glochidia with native versus non‐native fishes in two distinct European regions. Subsequently, we projected the obtained host compatibility data into the recent progress of biotic homogenization and estimated the degree of host dilution.ResultsWe found significant differences in the ability of A. anatina glochidia to parasitize the native and non‐native fish species in both the central and peripheral parts of the mussel's distribution range. As a result, the increasing presence of non‐native species within fish communities across Europe likely significantly decreases the availability of the mussel's host. Biotic homogenization of host communities may interfere with general life history traits (host specificity) of their local affiliate species.Main conclusionsThis study demonstrates that the mixing of regional biotas may lead to an excessive loss of host availability even for host generalists, such as the freshwater mussel A. anatina, with potentially broad consequences for their population dynamics. Conservation strategies of endangered affiliate species need to incorporate the biogeographical context of host–affiliate relationships and particularly the consequences of biotic homogenization.