The microbial diversity of faecal communities co-existing with mega fauna is not well understood even though these faecal communities are critical for health and development. Additionally, the transfer of microbial taxa among host animals is little studied. Here, we used 16S sequences obtained from clone libraries to characterise the faecal microbiota of Weddell seals breeding in McMurdo Sound and at White Island, Antarctica. Faecal bacterial communities were dominated by four phyla; Actinobacteria (20 %), Bacteroidetes (13 %), Firmicutes (23 %), and Proteobacteria (13 %). We also used automated ribosomal intergenic spacer analysis to examine the dispersal of bacteria between populations of Weddell seals breeding at White Island and in McMurdo Sound. The Weddell seals at White Island are isolated by the Ross Ice Shelf from the larger population of Weddell seals breeding in McMurdo Sound. We found that the faecal bacteria communities of the seals at White Island had lower diversity and that the community composition was significantly different compared with the seals in the McMurdo Sound area.