An increasing number of exotic animals are causing ecological problems. Exotic species are often unintentionally introduced when they contaminate transplanted stocks of other organisms. Here, we report that exotic threespine stickleback populations (Gasterosteus aculeatus) were introduced into three Japanese crater lakes (Lake Towada, Lake Kussharo, and Lake Shikotsu), along with salmonids transplanted for aquaculture. Microsatellite analysis showed that the stickleback population in Lake Towada was genetically similar to the Aisaka Stream and the Aisaka Pond populations. Compilation of the data on the morphology and stomach contents of the Lake Towada, the Aisaka Stream, and the Aisaka Pond populations showed that significant shifts have occurred in the body size and the stomach content after colonization.Some of these changes may be related to an outbreak of the Schistocephalus parasite. These results suggest that extreme care should be taken when salmonids are transported between watersheds for aquaculture and that long-term monitoring of exotic species is essential for ecosystem management.