AbstractChemoautotrophic denitrification plays an important role in nitrogen removal and the formation of a greenhouse gas (N2O) in aquatic environments. Natural stable isotopes support the tracing of nitrogen sources and the identification of biogeochemical processes in field research. However, the isotopic characteristics of N2O produced during chemoautotrophic denitrification have not been investigated so far. In this study, we analyzed isotopic signatures of nitrate and N2O in sulfur‐ and thiosulfate‐dependent denitrifying enrichments obtained from freshwater lakes. Chemoautotrophic denitrification exhibited a nitrate isotope pattern similar to heterotrophic denitrification: the 18ε/15ε‐nitrate followed a ratio close to 1. However, chemoautotrophic denitrification produced N2O with lower δ15N, δ18O, and higher site preference (SP = δ15Nα‐δ15Nβ) values, compared to heterotrophic denitrification. The SP value, approximately 5.1‰, was characteristic in detecting chemoautotrophic denitrification driven by different sulfur forms. δ18O varied with specific electron donors, around 20‰ and 40‰ during sulfur‐ and thiosulfate‐dependent denitrification, respectively. The unique N2O isotope characteristics were likely regulated by nitric oxide reductases of Burkholderiaceae populations during sulfur‐dependent denitrification and Sulfurovum during thiosulfate‐dependent denitrification. These findings improve our understanding of N2O production processes and have important implications for predicting N2O emissions at a greater spatial and temporal resolution.