Anthropogenic introduction of non-native species and the subsequent spread of their accompanying pathogens can cause serious declines in native wildlife populations. The common carp Cyprinus carpio, which is distributed worldwide due to intensive human introduction, is of little concern for conservation. However, the recent discovery of its ancient lineage endemic to the Japanese Archipelago has brought awareness of the conservation significance of the Japanese strain because this strain appears to be threatened by non-native Eurasian strains that heavily colonize Japanese freshwater bodies. Another threat has been recently posed by a lethal emerging pathogen, Cyprinid herpesvirus 3 (CyHV-3), which has spread to Japanese populations of common carp since 2003. Here, we report a significant decline in the frequency of Japanese native carp mtDNA haplotypes in two of the five subpopulations in Lake Biwa, one of the major habitats of the Japanese strain, after mass mortality caused by an outbreak of CyHV-3. It is likely that the less susceptible non-native strains may have competitively eliminated the native strain. Our results suggest that the emerging pathogen and invasion of Eurasian strains may pose synergistic threats to Japanese native common carp.