Soil management for organic farming depends on the effects of soil microbial activities and aggregation. The seasonal changes were evaluated in the soil microbial community by fatty acid methyl ester (FAME) and total glomalin analysis in an organic farming system (OFS) with no-till management compared to those in a conventional farming system (CFS) with tillage and chemical amendments in a flooded paddy. The average concentrations of individual FAMEs and glomalin in the OFS were significantly higher than those in the CFS during rice-growing stages (p<0.001). OFS had significantly lower ratio of $cy17:0/16:1{omega}7c$ and higher ratio of monounsaturated fatty acids to saturated fatty acids compared with those of CFS (p<0.001), indicating that microbial stress decreased due to organic soil inputs and the lack of chemical amendments, whereas communities of Gram-negative bacteria in OFS soils were significantly larger than those in CFS soils (p<0.001). Gram-negative bacteria should be considered as potential factor responsible for the clear microbial community differentiation observed between the OFS and the CFS in flooded paddy fields.