Abstract Nitrous oxide (N2O) is a potent greenhouse gas mainly produced by incomplete denitrification in agricultural soils. The rhizosphere is a hot spot for denitrification and this study aimed to discern the relative importance of soil type and crop on the genetic N2O production and reduction potential in soil and root-associated communities in relation to denitrification activity. Based on a pot experiment with two agricultural soils planted with barley or sunflower, we showed that the effect of soil type overrode that of crop on both genetic and enzymatic potential. We also demonstrate niche differentiation between the nitrous oxide reductase genes nosZI and nosZII, with clade I dominating in the root-associated community and clade II in the soil.