Changes in the abundance of an endemic amphipod, Jesogammarus annandalei,that inhabits the profundal zone of Lake Biwa were examined from 1966 to 1999. The abundance of J. annandalei increased suddenly during the mid1980s and thereafter stayed at a level that was sevenfold higher than that before 1980. Compared with the amphipod in the 1960s, both the clutch and body size of the matured individuals decreased during the 1990s, which suggests that per capita food supply decreased. Thus, the increase in the abundance of J. annandalei appeared to be due largely to an increase in their survival rate and not their growth or reproduction rates. In accord with the increase in amphipod abundance, the fishery catch of an endemic gobiid fish species that is dominant in the profundal zone and preys on this amphipod as a major food, decreased dramatically during the mid1980s. These results suggest that long-term changes in abundance of J. annandalei in Lake Biwa are mainly regulated by fish predation rather than by food supply.