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Nitrification in agricultural soil is an important process for food production. In acidic soil, nitrification is however also considered to be a major source of N2O production. The nitrification rate largely depends on the community composition of ammonia-oxidizing organisms. To obtain a view of the nitrification rates and N2O emission situations in low pH soils in Southern China and understand their relations with the microbial community composition, here we conducted 15N tracer experiments and microorganism community composition analysis using four acidic agricultural soil samples collected in Southern China. A single dominant community (relative abundance >68%) of the ammonia-oxidizing bacteria and ammonia-oxidizing archaea was observed in the soils with pH = 4.81–6.02. A low amount of NO3–{\text{NO}}_{3}^{\mbox{--}} was produced from the nitrification in the strongly acidic soil (pH = 4.03), and the calculated nitrification rate in this soil was significantly lower than those of other soils with pH = 4.81–6.02. High N2O emissions but low 15N–N2O emissions were observed in the soil with pH = 4.03. Our results suggest that, under aerobic conditions, soil pH is an important factor affecting nitrification through modifying the microorganism composition.