In this study, hypervariable region I (HVRI) of the mitochondrial DNA (mtDNA) control region, and five microsatellite loci were used to assess genetic variability and the extent of hybridization between the two fur seals (Arctocephalus tropicalis and A. gazella), that occur on Sub-Antarctic Marion Island. Both species were harvested during the 18th and 19th centuries, leading to a reduction in population size and the extinction of A. gazella at some localities. Whilst both species have recovered and are increasing in size, it is not clear to what extent sealing has affected genetic variation, although a more pronounced effect would be expected for A. gazella, given the more intensive harvesting of this species. The current study confirmed this hypothesis and revealed that A. gazella had a nucleotide diversity of 2.9 % whilst for A. tropicalis it was 4.2 %, across the HRVI mtDNA region sequenced. For microsatellite DNA, genetic variation in A. tropicalis was higher than in A. gazella in terms of the total number of alleles detected and the level of heterozygosity (HE=0.875, HO=0.845, mean number of alleles=13.6 and HE=0.799, HO=0.781, mean number of alleles=13, respectively). Diversity in both species is among the highest recorded in pinnipeds to date, and suggests that sealing did not overly affect the levels of genetic variation in these species. In terms of population structure, A. tropicalis show a high level of population structure, as indicated by the ΦST of 0.32 between Marion and Gough Island. Furthermore, the A. tropicalis haplotype tree comprising individuals from Marion, Iles Crozet, Gough, and Amsterdam islands, recovered three divergent evolutionary lineages with bootstrap values of 86% and 98%, for two of these lineages, indicating strong genetic structure and independent evolution. Shared haplotypes between Marion and other islands confirmed genetic exchanges, whilst the grouping of Marion and Gough Islands together is indicative of regular migration between these two islands. For A. gazella, the haplotype tree recovered numerous instances of grouping of individuals from Marion and Bouvetøya Islands confirming the hypothesis Bouvetøya is likely source of immigrants to Marion Island. This was further confirmed by low population differentiation between these two islands (FST = 0.062 and ΦST of 0.08). The level of hybridization between these species was low at Marion Island with only one hybrid being detected among the 134 animals for which mtDNA data were generated, corresponding to 0.75%. The same individual was identified as a hybrid, following microsatellite profiling of 146 animals, corresponding to a hybridization estimate of 0.68 %. This hybrid individual was classified phenotypically as A. gazella and genotypically was shown to have A. tropicalis ancestry. This level of hybridization is low compared to the other islands where the two species co-occur. However as the samples used in this study were primarily collected from species-specific sites, this may be an underestimate, and the studies focusing on sites where they are known to occur symaptrically, may yield higher estimates.