Isotopomer ratios of N2O (bulk nitrogen and oxygen isotope ratios, δ15Nbulk and δ18O, and intramolecular 15N site preference, SP) are useful parameters that characterize sources of this greenhouse gas and also provide insight into production and consumption mechanisms. We measured isotopomer ratios of N2O emitted from typical Japanese agricultural soils (Fluvisols and Andisols) planted with rice, wheat, soybean, and vegetables, and treated with synthetic (urea or ammonium) and organic (poultry manure) fertilizers. The results were analyzed using a previously reported isotopomeric N2O signature produced by nitrifying/denitrifying bacteria and a characteristic relationship between δ15Nbulk and SP during N2O reduction by denitrifying bacteria. Relative contributions from nitrification (hydroxylamine oxidation) and denitrification (nitrite reduction) to gross N2O production deduced from the analysis depended on soil type and fertilizer. The contribution from nitrification was relatively high (40%–70%) in Andisols amended with synthetic ammonium fertilizer, while denitrification was dominant (50%–90%) in the same soils amended with poultry manure during the period when N2O production occurred in the surface layer. This information on production processes is in accordance with that obtained from flux/concentration analysis of N2O and soil inorganic nitrogen. However, isotopomer analysis further revealed that partial reduction of N2O was pronounced in high-bulk density, alluvial soil (Fluvisol) compared to low-bulk density, volcanic ash soil (Andisol), and that the observed difference in N2O flux between normal and pelleted manure could have resulted from a similar mechanism with different rates of gross production and gross consumption. The isotopomeric analysis is based on data from pure culture bacteria and would be improved by further studies on in situ biological processes in soils including those by fungi. When flux/concentration-weighted average isotopomer ratios of N2O from various fertilized soils were examined, linear correlations were found between δ15Nbulk and δ18O, and between SP and δ15Nbulk. These relationships would be useful to parameterize isotopomer ratios of soil-emitted N2O for the modeling of the global N2O isotopomer budget. The results obtained in this study and those from previous firn/ice core studies confirm that the principal source of anthropogenic N2O is fertilized soils.