Bacteria dominate the remineralization of organic carbon in marine systems. Examining patterns of abundance, diversity and distribution is critical to understanding the contribution of bacteria to global biogeochemical cycles. In the oligotrophic deep sea, the role of bacterial communities is intimately linked to the flux of organic matter from primary productivity in surface waters. Deep-sea sediments are a major site of nutrient regeneration, supporting bacteria that comprise up to 90% of the benthic biomass and account for almost 45% of all respiration that occurs in the deep sea. The study of benthic bacterial communities in relation to organic matter flux may help to further scientific understanding of the contribution of bacteria to trends in the carbon cycle that have global significance. In this study, the bacterial abundance and diversity in deep-sea sediments beneath two zones of contrasting productivity in the Southern Ocean were compared. Sediments were taken at two abyssal sites, to the east and south of the Crozet Island Archipelago, in the Indian Ocean sector of the Southern Ocean. To the east of the islands, enhanced productivity levels are generated by seasonal blooms in marked contrast to the southerly, oligotrophic site where high nutrient, low chlorophyll conditions, predominate. Bacterial abundance was examined in sediment to a depth of 20 cm. No significant difference in abundance was found between sites, although a trend in decreasing abundance with vertical sediment depth was observed. Fluorescence in situ hybridisation (FISH) showed consistent distribution of different bacterial groups at both sites, where the gamma- and alpha-Proteobacteria were dominant. Similar denaturing gradient gel electrophoresis (DGGE) profiles were observed for both sites. A comparison of the eutrophic and oligotrophic surface sediment clone libraries found that approximately 36% of operational taxonomic units were common to both sites, however, richness was higher at the oligotrophic site. The results indicated a consistency in abundance and community structure between the two sediments, which may reflect shared biogeochemical characteristics. Both sites supported the same dominant community members. Differences in richness were observed between sites among the less dominant bacteria and these differences might reflect the contrasting productivity regimes of the overlying water.