DNA sequences of the mitochondrial control region of 180 North Atlantic right whales (Euhalaena glacialis) and 16 South Atlantic right whales (E. australis) have been determined using a combination of direct DNA sequencing and single stranded conformation polymorphism (SSCP) analysis. Five haplotypes were found in E. glacialis, and 10 in E. australis, but none were shared, supporting the reproductive isolation and separate species status of the North and South Atlantic right whales. One haplotype in E, glacialis was found in only three males born before 1982 and this matriline will likely be lost soon. The nucleotide diversity estimates for the five North Atlantic right whale haplotypes was 0.6% and 2.0% for the 10 haplotypes found in the South Atlantic right whales. The average haplotypic diversity was 0.87 in E. glacialis and 0.96 in E. australis, which is consistent with other studies showing a lower level of genetic variation in the North Atlantic right whale. Phylogenetic analysis identified two major assemblages of haplotypes in E. australis from the samples collected from Peninsula Valdes, suggesting a mixing of two historically divergent populations. Using genetic distance measurements with a divergence rate of 0.5%–1.0%/myr, we estimate E. glacialis diverged from E. australis 3–12.5 mya.