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Abstract Sediment nitrogen fixation and associated functional gene in the East China Sea were investigated using nitrogen-isotope tracing and molecular techniques. Potential rates of nitrogen fixation were detected, with values of 0.06–5.51 nmol N g−1 h−1. Abundance of functional gene (nifH) ranged from 0.36 × 106 to 5.39 × 107 copies g−1. Nitrogen fixation rates were not related to the abundance of nifH gene but to temperature, salinity, sulfide, iron and C/N, indicating that the sediment properties rather than microbial abundance dominated the nitrogen fixation. It is also estimated that sediment nitrogen fixation annually contributed about 3.43 × 105 to 3.10 × 107 tons nitrogen to the East China Sea, which accounted for 8.2–22.6% of the total inorganic nitrogen input. Overall, this study highlights the importance of benthic nitrogen fixation in controlling nitrogen budget in the East China Sea and improves our knowledge on nitrogen cycling in the coastal marine environments. Highlights • Occurrence of benthic nitrogen fixation is detected in the East China Sea sediments. • Benthic nitrogen fixation is associated closely with sediment properties. • Benthic nitrogen fixation plays an important role in controlling nitrogen budget. [ABSTRACT FROM AUTHOR]