The southern elephant seal (SES), Mirounga leonina, was intensively harvested during the 18th and 19th centuries, though never reduced to the levels seen for the northern species (Mirounga angustirostris). Although a number of putative populations occurring within the species’ circumpolar distribution in the Southern Ocean have been genetically assessed, no data was previously available for the Marion Island population. This study integrates Marion Island into the broader database by genetically profiling individuals with 9 microsatellite DNA loci (n = 73) and a single mitochondrial DNA (mtDNA, n = 68) locus corresponding to hypervariable region I (HVRI) of the non-coding displacement loop (D-loop). These data were then combined with existing haplotype datasets from five island populations, namely Heard Island, Peninsula Valdés, Macquarie Island, South Georgia, Elephant Island, and Sea Lion Island breeding colonies, and with comparable microsatellite typing data from four populations, namely Peninsula Valdés, South Georgia, Elephant Island and Sea Lion island, respectively, permitting inter-population level comparisons. Genetic variation of the Marion Island population was high for both microsatellite and mtDNA and consistent with levels previously reported for the other populations, with the exception of Peninsula Valdés (Argentina) where diversity levels are low. Forty polymorphic sites defined 44 mtDNA haplotypes from 68 Marion Island individuals. Of the 44 sequence haplotypes, three were shared with Sea Lion Island, one with Elephant Island, two with Heard Island and one with Macquarie Island. From the microsatellite data, it was found that Marion Island, like most other SES populations, had no private alleles. The one exceptional population is that at Sea Lion Island which has several private alleles at two loci. Marion Island was significantly differentiated from each of the other breeding colonies included in the study based on FST analyses for both microsatellite and mtDNA data. The magnitude of genetic differentiation between Marion Island and the South Georgia, Sea Lion and Elephant Islands was somewhat higher than that previously reported when the latter three islands were compared, but considerably less than the differentiation found between Marion Island and either Peninsula Valdés or Macquarie Island. Though the two markers showed similar trends with respect to population structuring, the pairwise differentiation at microsatellite loci was an order of magnitude lower than that of mtDNA, suggesting more frequent male-mediated gene flow between putative populations than female-mediated gene flow. Higher male dispersal was also confirmed by migration rate estimates from the microsatellite data compared to estimates from the mtDNA locus. These data are consistent with the earlier interpretation that most putative island populations show moderate levels of differentiation not directly related to geographic distance, while the mainland population in Argentina and the population at Macquarie Island stand out as being highly differentiated from the rest.