The North Atlantic right whale (Eubalaena glacialis) is the most endangered large whale in the world and shows few signs of recovery despite over 60 years of protection. In contrast, the South Atlantic right whale (E. australis), a closely related species, appears to be recovering successfully. Using DNA extracted from skin biopsy samples and two hypervariable minisatellite probes, we compared the levels of genetic diversity within the two populations. Our results revealed that unrelated North Atlantic (NA) right whales exhibit significantly less genetic variation than unrelated South Atlantic (SA) right whales (Jeffreys 33.15 (J33.15) probe: SNA-U-observed = 0.56 versus SSA-U-observed = 0.37, p < 0.01; M13 probe: SNA-U-observed = 0.74 versus SSA-U-observed = 0.46, p < 0.01). The level of band sharing among unrelated North Atlantic right whales was greater than that predicted for second-degree-related South Atlantic right whales (J33.15: SNA-U-observed = 56 versus SSA-2°-expected = 0.53, p < 0.05; M13: SNA-U-observed = 0.74 versus SSA-2°-expected = 0.60, p < 0.01), indicating that the northern animals have lost a substantial amount of genetic variability. Observed band sharing among North Atlantic first-degree relatives was lower than expected, based on band sharing among unrelated animals (J33.15: SNA-1°-observed = 0.67 versus SNA-1°-expected = 0.78, p < 0.01; M13: SNA-1°-observed = 0.83 versus SNA-1°-expected = 0.87, p = 0.15). This suggests that the matings between closely related individuals that would have resulted in the higher band-sharing values were unsuccessful. These results, in conjunction with behavioral and population data which indicate that North Atlantic right whales may be suffering from reduced fertility, fecundity, and juvenile survivorship, support the hypothesis that inbreeding depression is influencing the recovery of this species.