Soil microbial communities may be strongly influenced by agricultural practices, which change the soil environment. One such practice is the use of organic amendments, which increase carbon availability to microorganisms. PLFA profiles provide a robust measure that can be used to fingerprint the structure of soil microbial communities, and measure their biomass. Therefore, the PLFA analysis was used to investigate the microbial ecology of organic management soils in Korea and to determine how the duration of organic land use relates to microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility. Principal component analysis clearly separated organic and conventional soils. Multivariate analysis of PLFAs demonstrated that the duration of organic land use had a little significant impact on microbial community structure. This study suggested that PLFA analysis might be a better tool for assessing community differences and attempting to correlate changes of microbial community with soil fertility.