Elvers of intra-annual cohort of Japanese eel (Anguilla japonica) were sampled from northern, central, and southern estuaries of Taiwan in between December 2008 and February 2009, and examined for the population genetic structure by means of microsatellite analysis. All of the microsatellite loci were variable among 18 sample sets. Among them, AJMS-2 loci was more variable with 16 ~ 25 alleles; but AJMS-3 loci was less variable with 4 ~ 7 alleles. The average numbers of alleles for the 5 loci were scattered in a small range of 13.0 ~ 16.0, and the expected heterozygositywas 0.581 ~ 0.944. All values of pairwise FST for the 18 samples were low (≦0.0089), and non-significant (p > 0.0003), and the overall genetic differentiation was also very low and non-significant (FST = 0.0006, p = 0.418). This suggested that Japanese eel in Taiwan is a panmixic population.