Fatty acid methyl ester (FAME) profiles were used to describe differences in soil microbial communities influenced by conventional farming system (CFS), conventional farming system without pesticides (CFSWP), and organic farming system (OFS) for strawberry cultivation in controlled horticultural land. In comparison to the CFS soils, the average soil microbial biomasses of in the OFS soils were approximately 1.2 times for total FAMEs ($195nmol;g^{-1}$), 1.4 times for total bacteria ($58nmol;g^{-1}$), 1.5 times for Gram-negative bacteria ($27.3nmol;g^{-1}$), 1.2 times for Gram-positive bacteria ($26.1nmol;g^{-1}$), and 1.5 times for actinomycetes ($2.8nmol;g^{-1}$). The microbial communities of total bacteria (p<0.05) and Gram-negative bacteria (p<0.05) in the OFS and CFSWP soils were significantly higher larger than those in the CFS soils. However, fungal structure was significantly greater in CFS than in OFS and CFSWP (p<0.05). In principal component analyses of soil microbial communities, our findings suggest that actinomycetes should be considered as potential factor responsible for the clear microbial community differentiation observed between OFS and CFS in controlled horticultural land.