Based on a time series of ocean climate indices and catch records for seven pelagic fish species in the Tsushima Warm Current (TWC) and Kuroshio-Oyashio Current (KOC) regions from 1910 to 2004, we detected regional synchrony in the long-term fluctuations of the fish populations and identified alternation patterns of dominant species related to climate shifts. The annual catches of Pacific herring, Japanese sardines, Japanese anchovies, jack mackerel, chub mackerel, Pacific saury and common squid in the TWC region fluctuated in phase with those in the KOC region, which suggests that they were controlled by the same basin-wide climate forcing. After the collapse of the herring fishery, the alternation sequence was: sardines (1930s), Pacific saury, jack mackerel, common squid and anchovies ($1950s{sim}1960s$), herring ($late;1960s{sim}early;1970s$), chub mackerel (1970s) and then sardines (1980s). As sardine biomass decreased in the late stages of the cool regime, catch of the other four species increased immediately during the warm period of the 1990s. Regional differences in the amplitude of long-term catch fluctuations for the seven pelagic fishes could be explained by regional differences in availability, fishing techniques and activity.