Abstract:[Objective] To further understand the community structure, distribution, and ecological function differentiation mechanism of anammox bacteria in the groundwater of red soil areas. [Methods] We employed physical and chemical tests and high-throughput sequencing to study the microbial community structure, distribution of anammox bacteria, and their influencing factors in the groundwater of Ji’an. [Results] The nitrogen content exceeded the limit at three sites among the 11 groundwater sampling sites, with an over-limit rate of 27.3%. The water quality of only two sites met the requirements of the Standard for Drinking Water Quality (GB 5749—2022), which indicated an over-limit rate of 81.8%. Anammox bacteria presented wide distribution in groundwater, and the abundance of hzsB gene in the 11 samples ranged from 3.67×104 copies/g to 6.62×108 copies/g. Compared with other habitats, the groundwater in red soil areas showed increased copy number of functional genes of anammox bacteria, which indicated that the environmental characteristics of groundwater were more suitable for the growth and metabolism of anammox bacteria. Four genera of anammox bacteria were detected at each site. Specifically, Candidatus Brocadia, Candidatus Scalindua, Candidatus Jettenia, and Candidatus Kuenenia showed the average abundance of 62.47%, 17.44%, 14.41%, and 5.67%, respectively. The correlation analysis suggested that the gene abundance of anammox bacteria was significantly correlated with ammonia nitrogen, manganese, and chloride, which indicated that the increases in ammonia nitrogen, manganese, and chloride in groundwater may enhance the activity and abundance of anammox bacteria. [Conclusion] The results of this study highlight the importance of anammox bacteria in the geochemical and biological cycling of elements in the groundwater of red soil areas, which will provide basic data for the bioremediation of groundwater pollution in the red soil areas of China.