In order to understand the distribution of nirS and nirK denitrifying bacteria in rice roots. High-throughput sequencing of nirS and nirK denitrification functional genes in rice roots was carried out by using MiSeq sequencing platform. Bioinformatics analysis was carried out to reveal the distribution characteristics of nirS and nirK denitrifying bacteria in rice roots. The results showed that although the species richness of nirK-type denitrifying bacteria was higher than that of nirS-type denitrifying bacteria, the species distribution uniformity of nirK-type denitrifying bacteria was lower than that of nirS-type denitrifying bacteria. nirS and nirK denitrifying bacteria belong to 26 genera, 12 orders and 3 phyla, 5 classes. At the phylum level, proteobacteria is the common predominant phylum of nirS and nirK denitrifying bacteria. At the class level, alphaproteobacteria is the common dominant class of nirS and nirK denitrifying bacteria. Rhizobium is the dominant order of nirS denitrifying bacteria and Rhizobium is the dominant order of nirK denitrifying bacteria. At genus level, magnetospirillum is the dominant genus of nirStype denitrifying bacteria, while bosea, rhodopseudomonas, bradyrhizobium are the dominant genus of nirK-type denitrifying bacteria. The distribution characteristics of nirS and nirK denitrifying bacteria in rice roots ars consistent with the results of similar studies in other geographical environments. Five groups of bacteria such as Azospira existed only in nirS denitrifying bacteria, and 17 groups of bacteria such as Bosea existed only in nirK denitrifying bacteria, showing a special distribution.