[Objective] Microbial denitrification is the essential process to transform nitrate into nitrogen gas in estuarine environment. [Methods] In the present study, we investigated the diversity and distribution of the nirS-type and nirK-type denitrifying microbial communities in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea by Illumina MiSeq sequencing approach. [Results] A total of 346 nirS-type and 267 nirK-type Operational Taxonomic Units were detected. Environmental characteristics of sampling site and cluster analysis of nirS and nirK divided all Operational Taxonomic Units into hypoxic, southern and deep-water groups, and the samples from the deep-water group had the highest diversity of nirS functional genes. Furthermore, the dominant Operational Taxonomic Units phylogenetically formed several clusters, representing by Operational Taxonomic Units from distinct groups. All the dominant Operational Taxonomic Units were uncultured and some of them were first retrieved. Likewise, nirS gene was more adaptable to the hypoxic condition.[Conclusion] Our results indicate that widespread denitrifying microorganisms play a critical role in nitrogen cycle in the estuarine sediments.