Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A = 1.1, H(e) = 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P = 0.002), but simulations indicate low genetic diversity (H(e) < 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (F(IS) = 0.018) or population structure (K = 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to approximately 1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.