Genetic characteristics of sei whales, Balaenoptera borealis, inhabiting the western North Pacific were analyzed at 17 microsatellite loci in a total of 89 whales obtained from the area between 37 degrees N-45 degrees N and 147 degrees E-166 degrees E in 2002 (N=39) and 2003 (N=50). All the loci analyzed were polymorphic over the samples, some of the loci had more than 10 alleles, indicating a high level of genetic variation within samples. No significant deviation from the expected Hardy-Weinberg genotypic proportion was observed at the 17 loci in the samples. No evidence of genetic heterogeneity in allele frequencies was observed between sexes within samples as well as between the two temporally different samples, indicating a single population of sei whales inhabiting the western North Pacific. We finally tested and demonstrated that the population appeared not to suffer from genetic bottleneck as a result of population decline from past commercial whaling.