Laboratory study was conducted to follow the degradation and effect of pencycuron on microbial parameters of flooded alluvial (AL) soil (Typic udifluvent) and Coastal Saline (CS) soil (Typic endoaquept) under rice cultivation. Pencycuron degraded faster in CS soil and in soil amended with Decomposed Cow Manure (DCM). Pencycuron at field rate (FR), 2FR and 10FR affected the Microbial Biomass C (MBC), soil ergosterol content and Fluorescein Diacetate Hydrolyzing Activity (FDHA) differentially. The DCM amendment did not seem to have any counteractive effect on the toxicity of pencycuron on the microbial variables. The change in microbial metabolic quotient (qCO2) and microbial respiration quotient (QR), indicated that pencycuron induced disturbance at 10FR. Pencycuron was more toxic to the metabolically activated and newly generated soil microbial populations.