The crangonyctid amphipod, Crangonyx floridanus Bousfield, originating from North America (Florida), has invaded the freshwater habitats of Japan. This amphipod was first found in Japan in 1989, in the Furutone-numa oxbow lake of the Tone-gawa River which flows along the Ibaraki-Chiba prefectural boundary. Its strong capacity to adapt to broad and variable environmental conditions, and their superior reproductive efficiency have contributed to its rapid dispersion throughout Japan. These alien amphipods have a significantly broader range of habitats than their native counterparts, and can inhabit a wide range of environments, even those with a relatively high water temperature. They also readily inhabit the oligosaprobic waterways originally used by native species. In the present study, we conducted a comparative ecological and population dynamics research between the alien amphipod C. floridanus and the native amphipod Jesogammarus jesoensis, at the Tate-gawa River study site (Azumino, Nagano Prefecture). Although both the alien and native amphipods inhabit the same area, habitat segregation at the microhabitat level was observed (i.e., they tend to utilize different water plant species as their habitats). It was also suggested that some interaction may be occurring in terms of the timing of their reproductive season in order to facilitate their successful cohabitation. No evidence of a particularly strong competitive relationship was observed between the alien and native amphipod species. This is thought to be due to their niche segregation as a result of the significant differences in their body size, and also to the abundant availability of habitats and food (i.e., rich water plants), along with the high water quality of the environment at the Tate-gawa River study site.