Commercial exploitation reduced the North Atlantic right whale (Eubalaena glacialis) population from c. 12 000 in the 11th century to around 300 by the 21st century. We examine the effect of this population decline on levels of genetic variation at 16 microsatellite loci and contrast levels of variability to that in a closely related species (E. australis). Of the 13 loci developed from the E. glacialis genome, 100% were polymorphic in E. australis. In contrast, nine loci were polymorphic in E. glacialis and four were fixed. Both allelic diversity (A) and heterozygosity (H) were significantly lower in E. glacialis than E. australis (A = 3.2 ± 2.6 vs. A= 6.9 ± 3.3, P < 0.001; H= 0.31 ± 0.25 vs. H= 0.72 ± 0.23, P < 0.001, respectively). Bottleneck anlayses indicate that the population is in mutation-drift equilibrium and that a genetic bottleneck did not occur during the most recent decline (18th–20th centuries). Nevertheless, low frequency alleles are relatively uncommon in E. glacialis, suggesting that genetic variability has been reduced in this population. Possible origins of low genetic variability are discussed, including the slow but continual erosion of alleles during the 800-year period of decline.