The seasonal patterns of the denitrifiers (denitrifying bacteria) in the sediment of Daya Bay, southern China, were examined using quantitative PCR and high-throughput MiSeq sequencing methods in spring, summer and winter. The abundance and diversity of nirS-encoding denitrifiers were much higher than that of nirK-encoding denitrifiers, indicating that the former probably dominated the denitrification processes in sediments of Daya Bay. The average abundance and diversity of nirS-encoding denitrifiers were much higher in spring than that in summer and winter, on the other hand, the abundance of nirK-encoding denitrifiers showed the opposite pattern. The species composition of nirS-encoding denitrifiers community in spring differed significantly from that in summer and winter, whereas, no significant difference existed between summer and winter. The dominant environmental drivers for the diversity of community species were NO2-, NO3- and DO concentrations. The abundances of dominant genera of nirS-encoding denitrifiers, Accumulibacter sp. and Cuprizvidus sp., were significantly higher in summer and winter than that in spring, and were negatively correlated with NO2-, NO3-, and DO concentrations ( p < 0.05). In contrast, the abundances of Azoarcus sp. and Halomonas sp., were highest in spring, and were positively correlated with NO3- and NO2- content (p < 0.05). For nirK-encoding denitrifiers, a significant difference in community composition was observed between spring and winter. No obvious correlation was found between community composition of nirK-encoding denitrifiers and environmental parameters.