Habitat fragmentation imposes multiple detrimental effects on wild populations, such as reducing population size and connectivity. Here, I show for the first time that habitat fragmentation also promotes inter-specific hybridization. Salmonid fishes have external fertilization, which increases the chance of hybridization. In the wild, however, reproductive isolation generally operates through the shifts in breeding timing, area and behavior. Sympatric charrs (Dolly Varden and white-spotted charr) in the Sorachi River in central Hokkaido, Japan, rarely produce their hybrid probably because Dolly Varden spawn later in the season and upper reaches of streams although they are partially overlapped. Microsatellite analysis suggested that the rate of natural hybridization was much less than 1% for the sympatric charrs. However, in tributary streams fragmented by erosion-control dams, hybridization rate was 10-50 times higher than non-fragmented streams. Post-F1 hybrids were also suggested. This result indicates that spawning area of Dolly Varden was confined to lower stream reaches where mature white-spotted charr can approach. Because dams are ubiquitous all over the world, similar disturbance may exist many river systems.