In the Ross Sea region of Antarctica, ornithogenic soils form on land under Adélie Penguin rookeries. Compared with mineral soils of the Ross Sea region, ornithogenic soils are generally high in microbial biomass, organic carbon, and total nitrogen and phosphorus, with high electrical conductivity and large variations in pH. The objective of this study was to assess the bacterial composition of ornithogenic soils from Cape Hallett and Cape Bird in the Ross Sea region using culture-independent methods. Soil clone libraries were constructed and those clones that occurred > or = 3 times were sequenced. The bacterial diversity of the soils was dependent on the presence of penguins. Firmicutes most closely related to the endospore-formers (e.g., Oceanobacillus profundus and Clostridium acidurici) and (or) Gammaproteobacteria belonging to the genus Psychrobacter dominated soils currently occupied with penguins. In contrast, Gammaproteobacteria, closely related to cultured members of the genera Rhodanobacter, Psychrobacter, Dokdonella, and Lysobacter, dominated the soils previously colonized by penguins. Results of this study indicate that despite relatively high nutrient levels and microbial biomass, bacterial communities of ornithogenic soils were not more diverse than those of mineral soils of the Ross Sea region of Antarctica.