Abstract Type and amount of nutrient inputs to cultivated soils may alter microbial community structure and activities, which could greatly influence their environmental fate. This study compared no fertilizer (NF), chemical fertilizer (CF), CF+pig manure (CFM) and CF+straw manure (CFS) for microbial dynamics in alluvial paddy soil (Typic Eduoagulpt). Microbial communities were characterized by dilution plate technique, Biolog tests and phospholipid fatty acid (PLFA) profiles. Biolog plates data indicated that soil microbial metabolism quotient, Shannon index and McIntonsh index increased significantly in CFS- and CFM-treated soils relative to that in NF soil. Soil PLFA analysis demonstrated that molar ratios of bacterial monounsaturated fatty acids (15:1ω6c, 16:1ω7c, 16:1ω9c, 18:1ω7c, 18:1ω9c) and fungal polyunsaturated fatty acid (18:2ω6,9c) were greater in CFM- and CFS-treated soils. Saturated straight chain lipids 14:0, 17:0, 18:0, 19:0 and 20:0 (representing actinomycetes) were higher in NF- and CF-treated soils. These results indicated that organic matter inputs increased the PLFA biomarkers for bacteria and fungi, but reduced that for actinomycetes. Ratio of Gram-positive to Gram-negative bacteria was significantly higher in NF- and CF-treated soils (P≤0.05). It concludes that organic manures enhance the bacterial and fungal communities rather than actinomycetes; whereas, impact of chemical fertilizers was vice versa indicating deficiency of organic carbon and nutrients in the soil. Further, actinomycetes and G +ve bacteria seem to be the indigenous microbiota of paddy soil, which was dominated by G −ve bacteria and fungi after the addition of organic manures.