In flooded paddies, peak greenhouse gas nitrous oxide (N2O) emission after rewetting the dry soils is well known, but the relative contribution of biotic and abiotic factors to the emission is still unclear. In this study, we used the isotope technique (δ18O and δ15NSP) and molecular-based microbial analysis in an anoxic incubation experiment to evaluate the contributions of bacterial, fungal, and chemical denitrification to N2O emissions. We collected eight representative paddy soils across China for an incubation experiment. Results show that total N2O accumulations during the 10-day incubation period were mainly produced by fungal denitrification (58-77%) in six out of the eight investigated flooded paddy soils. The contribution of fungal denitrification was equal to or less than those of bacterial and chemical denitrification in the other two soil types. Moreover, around 11-35% of the total N2O emissions were derived from chemical denitrification in all soil types, suggesting its important role in N2O production. We further found that the initial soil organic carbon was the main regulator for the pattern of N2O sources. Microbial interactions and gene expressions could also be the potential explanation rather than denitrifier community composition. Overall, these findings highlight the dominance of the fungal denitrification pathway for N2O production in flooded paddy soils. This suggests that fungal contribution should be considered when optimising agricultural management system timing to control N2O emissions in flooded paddy soil ecosystems, and for the relevant establishment of predictive numerical models in the future.