The catadromous Japanese eel has an unusual life history. Controversy remains, however, as to whether its population structure is characterized by panmixia or genetic differentiation. Migration patterns are considered an important factor in determining a species' population structure. Eight polymorphic microsatellite loci were used as genetic markers through which we were able to reject the null hypothesis of panmixia. Slight genetic differentiation between these populations was determined by Wright's and Slatkin's fixation indices, F ST and R ST statistics adjusted using Bonferroni's correction. Although isolation-by-distance is often observed in marine species, the present result is thought to follow the member-vagrant migratory hypothesis. The metapopulation model fits the elver recruitment strategy according to results of the high probability of assignment test. The UPGMA tree showed the Japanese eel populations as being divided into 2 groups: a low-latitude group (Shantou in South China, and Tanshui and Fangliao in Taiwan) and a high-latitude group (Mikawa Bay in Japan, Daecheon-myon in Korea, and the Yalu River and Hangzhou in Northeast China). Temporal genetic variations indicate that most progeny return to similar habitats where their ancestors formerly resided. There was a high correlation (AMOVA; p < 0.05) when the Japanese eel was divided into the 2 management units (high-and low-latitude groups). These units will be useful when applied to fisheries conservation and management in the northwestern Pacific Ocean.