Nitrite-dependent anaerobic methane oxidation (n-damo) process can play an important role in the methane mitigation in the environment. However, the distribution of n-damo organisms in freshwater sediment ecosystem and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment n-damo community in the freshwater Dongjiang River using quantitative PCR assay and clone library analysis targeting n-damo pmoA gene. Sediment samples were collected at nine locations along the Dongjiang River in May and August in 2015. The remarkable temporal and spatial changes of sediment n-damo community abundance, richness, diversity, and structure occurred in the Dongjiang River and its tributaries. The n-damo pmoA gene in sediments of the Dongjiang River and its tributaries varied from 9.07 x 10(4) to 3.02 x 10(6) copies per gram dry sediment. Compared to the stem of the Dongjiang River, tributaries had relatively higher sediment n-damo community size. Sediment n-damo community abundance was higher in August than in May, while an opposite trend was observed for n-damo community richness and diversity. Sediment n-damo community structure showed a great difference between in May and August. Sediment nitrite nitrogen content was positively correlated to n-damo community abundance, but negatively to richness and diversity. Ammonia nitrogen content showed a positive correlation to n-damo community abundance, while n-damo community diversity was negatively correlated to the ratio of total organic carbon to total nitrogen (C/N). In addition, nitrite nitrogen as well as C/N might influence n-damo community structure.