The effects of sediment hypoxia, resulting from increased carbon loads or decreased dissolved oxygen (DO), on nitrogen cycling in estuarine environments is poorly understood. The important role played by bacterial and archaeal ammonia oxidizers in the eventual removal of nitrogen from estuarine environments is likely to be strongly affected by hypoxic events. In this study, an analysis of the effects of different levels of sediment hypoxia (5%, 20% and 75% DO) was performed in a microcosm experiment. Changes in the nutrient fluxes related to nitrification at 5% DO were observed after 4 h. Quantification of the key nitrification gene ammonium monooxygenase (amoA) in both DNA and RNA extracts suggests that bacterial amoA transcription was reduced at both of the lower DO concentrations, while changes in DO had no significant effect on archaeal amoA transcription. There was no change in the diversity of expressed archaeal amoA, but significant change in bacterial amoA transcriptional diversity, indicative of low- and high-DO phylotypes. This study suggests that groups of ammonia oxidizers demonstrate differential responses to changes in sediment DO, which may be a significant factor in niche partitioning of different ammonia oxidizer groups.