Genetic relationships among 4 Steller sea lion (Eumetopias jubatus) rookeries in the Kuril Is. (Brat Chirpoev, Lovushki, Raykoke, and Antsiferov Is.) and 1 at Iony I. were evaluated using an inter-simple sequence repeat (ISSR)-polymerase chain reaction assay. An ISSR primer yielded 15 amplification products, almost all of which were polymorphic. An analysis of molecular variance test revealed that 94.4% of the total genetic variation was attributable to differences among individuals within rookeries, and 5.6% was attributable to those among rookeries (Ф(subscript ST)=0.056). Pairwise Ф(subscript ST) values were relatively high between rookeries of the Kuril Is. and that on lony I., while no significant genetic differentiation was detected among rookeries of the Kuril Is. Since previous research using mitochondrial DNA markers revealed the presence of unique haplotype(s) on each island of the Kuril Is., our results suggest that males, rather than females, contribute to gene flow among the islands.