The physicochemical properties, aerobic and anaerobic bacterial population in alluvial and acid sulphate soils and roots of rice plants were studied in the present study. There was slight variation in pH of soil from 5.47 in alluvial soil to 5.15 in acid-sulfate soil.Higher organicmatter content was observed in pokkali than alluvial soil. The total nitrogen and sulfate are higher in alluvial soil, than pokkali. Flooded rice soils are predominantly with anaerobic environment with micro sites of nutrient poor or rich conditions. The total population of DNB bacteria in alluvial soil was considerable whereas the population of NB bacteria in flooded alluvial soil wasmore than that of the DNB bacteria under aerobic conditions. On the contrarily, DNB were dominated under anaerobic conditions. Flooded conditions are favorable for the growth of oligotrophic bacteria especially those capable of growing under anaerobic conditions. The anaerobic oligotrophic bacterial populationwas higher than the population of aerobic oligotrophic bacteria in the roots of rice plant.