Usage of pesticides improve the quantity and the quality of crops, but widespreadly use of pesticides inappropriately with residues in the environment has resulted in some adverse effect thar would cause pollution seriously and harm people indirectly. The present research was designed to assesment the potential of anaerobic degradation of Endosulfan and Butachlor by indigenous microorganisms of river sediment. Sediments collected from southern Taiwan of Er-Jen River basin were sampling separately at south coast, river course and north coast. Microbial degradation can proceed better in the presence of Organic chlorinated pesticides (OCPs) in the mixed culture, at concentrations between 0.5 to 100 μg mL-1, with 30 ℃ incubation temperature.GC-ECD was used to analysis residues of Endosulfan and Butachlor. Denaturing gradient gel electrophoresis (DGGE) was used for analyzing the bacterial community structures during pesticides degradation periods. According to the results, two experimental pesticides were more easily degraded under anaerobic conditions than those in sterilized medium. Degradation rates were faster for Butachlor under anaerobic conditions than Endosulfan, Endosulfan was more persistent than Butachlor. Incubation with applying 0.5~2 µg mL-1 Endosulfan after 25 days, α-type Endosulfan accomplished the degradation and β-type were degraded within 80 %, which showed that degradation rates of α-type Endosulfan were faster than β-type. Results from applying 50 µg mL-1 Endosulfan, after 90 days of incubation, β-type was analyzed to had 70 % of residues in sediments from south coast and river course, but 20 % from north coast, which showed that different sampling place of sediments had diverse ability of degradation. The best degradation activity was observed in the case of sediment from south coast with 2 µg mL-1 Endosulfan. Application of Butachlor with 0.5~5 µg mL-1 were degraded after 30 days of incubation under anaerobic conditions, while 100 µg mL-1 were degraded with 80 % within 60 days. According to the T1/2, the highest degradation activity was observed in the case of sediment from south coast with 2 µg mL-1 Butachlor. DGGE analysis of the 16S rDNA fragments obtained from mixed cultures indicated that microbial community structure was shifted during the incubation periods. Cluster analysis showed that the microbial community structures were significantly different after application of two pesticides. According to results, these bacteria may play significant roles during the OCPs degradation periods.