Anaerobic ammonium-oxidizing (anammox) bacteria are widely detected in diverse anoxic niches, but only a few studies have reported their presence in oil reservoirs. Here, we collated published clone library data of the 16S rRNA and hzo genes of anammox bacteria and high-throughput sequencing data of the 16S rRNA genes from microbial communities to identify anammox bacteria inhabiting oil reservoir environments. Furthermore, the community composition of anammox bacteria and nitrate-reducing bacteria (NRB) associated with dissimilatory nitrate reduction to ammonium (DNRA) in a water-flooded oil reservoir was investigated by metagenome sequencing. The combined results suggested the occurrence of anammox bacteria in oil reservoirs, however sequencing of the 16S rRNA genes and metagenome from microbial communities could not effectively detect them due to their low abundance in the overall community. The results also showed that anammox bacteria were more easily detected in the downhole of the water-injection wells rather than wellheads of injection and oil-production wells. The co-existence of denitrifying bacteria (DNB) reducing nitrate to N2O and N2, NRB associated with DNRA, and anammox bacteria in oil reservoirs supports a unique N cycling in such ecosystem and implies the potential reduction of externally injected nitrate into the oil reservoirs via the production of N2O and N2. This study improves our knowledge on efficient detection of anammox bacteria and highlights the roles of these bacteria in the nitrogen cycle in oil reservoirs.