The seasonal changes were evaluated in the soil microbial populations by selected media in an organic farming system (OFS) with no-till management compared to those in a conventional farming system (CFS) with tillage and synthetic amendments in a flooded paddy from 2009 to 2010. The populations of aerobic bacteria and fungi in the OFS were significantly higher than those in the CFS at the harvesting stages, whereas those of Gram-negative bacteria was significantly higher in the OFS than in the CFS before the submerging stages. In addition, populations of aerobic bacteria, Gram-negative bacteria, and fungi tended to rapidly decreased after the submerging stages may be due to insufficient oxygen. Gram-negative bacteria should be considered as potential factor responsible for the microbial population differentiation observed between the OFS and the CFS in flooded paddy fields.