The characteristics of the population genetic structure of the Japanese anchovy (Engraulis japonicus Temminck & Schlegel) were collected from the West, South and East Seas of Korea in August, 2006 and were compared using six microsatellite DNA loci. In the West Sea population, the range of allele number against 72 individuals was from 19 to 41, the average allele number was 28.5. In EJ9, the allele number had the highest value of 41, this was 1.4 times higher than the average number of allele. The average allele number of the South Sea population was 24.5 that was less than that of West Sea population. In EJ2, EJ9 and EJ27.1 loci, the allele number was higher than average allele number in the South Sea population. In the East Sea population, the average allele number was estimated at 25.0 that most of loci except for EJ35 were higher than average allele number. Allele frequency in the West, South and East Sea populations was below 0.24. The value of observed heterozosity for six loci was approximately 0.5 higher than that of expected heterozosity (p>0.05), but three populations similar values to these heterozosity. Although the genetic diversity was higher value of above 0.9, three populations had a similar value. Genetic differentiation and distance combined estimate of the six loci were 0.258 and 0.019 (p>0.05), respectively, but showed no significant distance between three populations. These results suggested that it is responsible for no differentiated gene pool between three populations.