Products from the protected East Sea/Sea of Japan (‘J’ stock) minke whales (Balaenoptera acuturostrata) are sold widely on the commercial markets of Japan and Korea despite the protection of this stock since 1986. To determine the minimum number of individual whales for sale, genotypes from six microsatellite loci were used to profile North Pacific (NP) minke whale products purchased on these markets between December 1997 and October 1999. Genotype differences showed that 99 NP minke whale products from the Japanese market represented 86 unique individuals. Of these, 33.7% were of likely J-stock origin based on mitochondrial (mt) DNA haplotypes. In Korea, genotyping showed that 23 NP minke products from March 1999 represented 18 individuals, and 19 products from October 1999 represented 16 individuals. No matches were found between the two sampling periods, giving a total of 34 unique individuals. A frequency-of-capture model suggests that 98 minke whales were present on the Korean market over the two brief sampling periods. No genotype matches were confirmed between the two countries, indicating that undocumented exploitation of this depleted stock must be additive, and greater than previously assumed.