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I developed and tested a protocol for determining the sex of individual pinnipeds using the sex-chromosome specific genes ZFX and ZFY. I screened a total of 368 seals (168 crabeater, Lobodon carcinophagus; 159 Weddell, Leptonychotes weddellii; and 41 Ross, Ommatophoca rossii) of known or unknown sex and compared the molecular sex to the sex assigned at the time of collection in the Ross and Amundsen seas, Antarctica. Discrepancies ranged from 0.0% - 6.7% among species. It is unclear, however, if mis-assignment of sex occurred in situ or in the laboratory. It also is possible, however, that the assigned morphological and molecular sex both are correct, owing perhaps to developmental effects of environmental pollution. I sequenced a portion (ca 475 bp) of the mitochondrial control region of Weddell seals (N = 181); crabeater seals (N = 143); and Ross seals (N = 41). I resolved 251 haplotypes with a haplotype diversity of 0.98 to 0.99. Bayesian estimates of Θ from the program LAMARC ranged from 0.075 for Weddell seals to 0.576 for crabeater seals. I used the values of theta to estimate female effective population sizes (NEF), which were 40,700 to 63,000 for Weddell seals, 44,400 to 97,800 for Ross seals, and 358,500 to 531,900 for crabeater seals. Weddell seals and crabeater seals had significant, unimodal mean pairwise difference mismatch distributions (p = 0.56 and 0.36, respectively), suggesting that their populations expanded suddenly around 731,000 years ago (Weddell seals) and around 1.6 million years ago (crabeater seals). Both of these expansions occurred during times of intensified glaciations and may have been fostered by expanding pack ice habitat. Autosomal microsatellite based NEs were 147,850 for L. Weddellii, 344,950 for O. rossii, and 939,600 for L. carcinophagus. I screened one X-linked microsatellite (Lw18), which yielded a larger NE estimate for O. rossii than the other two species. Microsatellite NE estimates are compared with previously published mitochondrial NE estimates and this comparison indicates that the Ross seal may have a serially monogamous system of mating. I find no sign of a recent, sustained genetic bottleneck in any of the three species.