Abstract: Background and Objectives: Identification of microbial community composition is very important for understanding the degradation kinetics of pollutants in water. This study was conducted to isolate and to identify the microbial communities of Kurose River water and to investigated the biodegradation kinetics of fenitrothion by identified microbial strains. Materials and Methods: Microbial community composition was investigated using differential display-denaturing gradient gel electrophoresis (DGGE). Identification of microbial isolates was carried out using 16S rRNA gene sequence analysis. Biodegradation of fenitrothion was carried out using High-performance liquid chromatography and gas chromatography-mass spectrometry analysis. Results: The results showed that the degradation of fenitrothion in Kurose River water occurred because of various bacterial isolates. Moreover, the degradation rate of fenitrothion in Kurose River water at different sampling sites depended on the microbial content and the chemical composition of the water. The bacteria isolated from the Kurose River identified as Pseudomonas putida and Flavobacterium sp. The degradation rate of fenitrothion by the isolated bacteria was lower in river water than in artificial growth media. The identified degradation products of fenitrothion were amino-fenitrothion and 3-methyl-4-nitrophenol. Conclusion: The microbial community and chemical composition of the Kurose River water significantly affect the fate and biodegradation kinetics of fenitrothion. Molecular identifications of microbial community structures of aquatic systems are very useful for interpretation of the fate and degradation kinetics of fenitrothion.