The soil microbial community controls the ecosystem functions of the soil. Changes in the soil microbial community can reflect changes in soil quality, and can be regarded as an early warning of changes in, and a sensitive indicator of the quality of, the soil ecosystem. Traditional methods for identifying soil microbes detect only 0.1%-10% of the microbes in the soil environment, and so they cannot accurately show the distribution of microorganisms in the soil. Phospholipid fatty acids (PLFAs) can be used as biomarkers to evaluate the diversity of the microbial community both qualitatively and quantitatively. The PLFA profiles differ among different groups of microbes, and PLFAs rapidly decompose after the death of microorganisms. Many researchers have found that the amount of PLFAs directly extracted from the soil can give an accurate estimate of the soil microbial biomass. Therefore, the aim of the present study was to explore the effects of the herbicide quinclorac on soil microbial community structures. Soil samples from non-flooded paddy soil and flooded paddy soil were supplemented with various concentrations of quinclorac [0 (control), 83.3, and 166.6 μg/kg dry soil] and kept in the dark at 25℃ for 60 days. The microbial community structures were then evaluated by PLFA analysis. Analyses of the PLFA profiles showed that quinclorac significantly affected the soil microbial community in both flooded and non-flooded paddy soils. In this study, the total PLFAs was considered to reflect the biomass of the microbial community; the bacterial biomass was reflected by the amount of 17-carbon ester chains, glycerol, and certain saturated and monounsaturated fatty acids (6:0, 11:0, 12:0, 13:0, 14:0, 14:1, 15:0, 15:1, 16:0, 16:1, 17:0, 17:1, 18:0, 20:0, 20:1, 22:0 and 22:1), while the fungal biomass was reflected by the amount of 18:1n9t, 18:1n9c, 18:2n6t, 18:2n6c, and 18:3n6. The non-flooded paddy soil treated with 83.3 μg/kg quinclorac showed decreases in the total microbial biomass, fungal biomass, and bacterial biomass. The microbial populations were even more strongly inhibited in the non-flooded paddy soil treated with 166.6 μg/kg quinclorac. Both concentrations of quinclorac resulted in decreased fungi/bacteria ratios in non-flooded paddy soil, which indicates that quinclorac treatments detrimentally affected the microbial stability of non-flooded paddy soil. For flooded paddy soil, treatment with 83.3 μg/kg quinclorac enhanced the total microbial biomass and fungal biomass, but inhibited certain components of the bacterial biomass. In the 166.6 μg/kg quinclorac treatment, the flooded paddy soil showed increased total microbial biomass, increased bacterial biomass, and increased fungal biomass. The fungi/bacteria ratios in flooded paddy soil in both of the quinclorac treatments did not differ from that of the control, which indicates that quinclorac did not interfere with the biological stability of flooded paddy soil. The PLFA principal component analysis indicated that the advantageous populations in both flooded paddy soil and non-flooded paddy soil were those containing 14:0, 15:0, 16:0, and 18:2n6c PLFAs. These findings could therefore be used to optimize soil microecological systems, and show that PLFA analysis is an accurate method to assess the diversity of the microbial community in soils.