Freshwater mussels are in decline worldwide, including in Australia, although not all species are equally affected. To better understand the low levels of abundance in a rare Australian species, Hyridella narracanensis, we compared the factors responsible for its distribution with a co-distributed common species, H. drapeta. Environmental and habitat specific factors demonstrated no difference between the two species suggesting that abiotic factors are not restricting the distribution of H. narracanensis, which should therefore be able to find suitable habitat across coastal Victoria. Population genetic analysis for both species using mitochondrial DNA (mtDNA) showed similar patterns of isolation between river catchments, which suggest that dispersal is somewhat limited in both species, although this does not explain the differences between the two. Glochidial (larval) release strategies differ substantially between the two species and suggest that H. drapeta is a host generalist while H. narracanensis is host-specific. Therefore it appears that biotic factors (namely host availability) resulting from host specificity appear to be key in explaining the narrow distribution of H. narracanensis distribution, particularly in the Yarra River catchment where many native fish species are in decline. Interestingly, in the course of this study, the genetic analysis provided very strong evidence that another mussel species, the critically endangered H. glenelgensis is likely to be a translocated population of H. narracanensis. Broader surveying of Victorian streams is required to accurately determine patterns of distribution in H. narracanensis, and in particular, the identification and conservation of the fish host(s) used by H. narracanensis is critical to protect the species from decline, extirpation, or extinction