Nitrate and nitrite denitrification rates were analyzed for 12 activated sludge samples collected from municipal wastewater treatment plants. Five of the 12 samples denitrified nitrite more rapidly than they denitrified nitrate. To evaluate the relationship between denitrification rates and denitrifier community structure, we analyzed nitrite reductase genes (nirK and nirS) for two samples. As a result, the activated sludge sample that denitrified nitrate more rapidly than it did nitrite showed large nirS diversity compared with the sample that denitrified nitrite more rapidly than it did nitrate. Moreover, the nirS populations of the two samples were phylogenetically different, although the nirK populations of the two were almost same.