Reproduction of native and invasive bitterling fishes and their hybridisation was studied in Japan. We collected mussels in which these bitterlings lay their eggs, kept them in aquaria, collected eggs/larvae ejected from mussels, and genotyped them. We found that hybrids occurred when local mussel density was low. The rapid decline of the host mussels and artificial introduction of an invasive congener interacted to cause the rapid decline of a native fish.