The relative importance of individual microbial pathways in nitrous oxide (N2O) production is not well known. The intramolecular distribution of 15N in N2O provides a basis for distinguishing biological pathways. Concentrated cell suspensions of Methylococcus capsulatus Bath and Nitrosomonas europaea were used to investigate the site preference of N2O by microbial processes during nitrification. The average site preference of N2O formed during hydroxylamine oxidation by M. capsulatus Bath (5.5 ± 3.5‰) and N. europaea (−2.3 ± 1.9‰) and nitrite reduction by N. europaea (–8.3 ± 3.6‰) differed significantly (ANOVA, f(2,35) = 247.9, p = 0). These results demonstrate that the mechanisms for hydroxylamine oxidation are distinct in M. capsulatus Bath and N. europaea. The average δ18O-N2O values of N2O formed during hydroxylamine oxidation for M. capsulatus Bath (53.1 ± 2.9‰) and N. europaea (−23.4 ± 7.2‰) and nitrite reduction by N. europaea (4.6 ± 1.4‰) were significantly different (ANOVA, f(2,35) = 279.98, p = 0). Although the nitrogen isotope value of the substrate, hydroxylamine, was similar in both cultures, the observed fractionation (Δ15N) associated with N2O production via hydroxylamine oxidation by M. capsulatus Bath and N. europaea (−2.3 and 26.0‰, respectively) provided evidence that differences in isotopic fractionation were associated with these two organisms. The site preferences in this study are the first measured values for isolated microbial processes. The differences in site preference are significant and indicate that isotopomers provide a basis for apportioning biological processes producing N2O. Copyright © 2003 John Wiley & Sons, Ltd.