The present study evaluated the changes of soil microbial communities that were subjected to no-till and compared the results to those subject to tillage for organic farming in a controlled horticultural field by fatty acid methyl ester. Fungi ( P<0.001), gram-positive bacteria ( P<0.001), arbuscular mycorrhizal fungi ( P<0.01), and actinomycetes ( P<0.01) in the no-till soils were significantly larger than those in the tillage soils. The no-till in the subsoil had a significantly lower ratio of cy17:0 to 16:1omega7c compared to that of tillage, indicating that microbial stress decreased because the soils were not disturbed ( P<0.05). Fungi should be considered as a potential factor responsible for the obvious microbial community differentiation that was observed between the no-till and tillage areas in a controlled horticultural field.