The environmental authority of Taiwan has announced that ocean quality standard A, with E. coli less than 1,000 CFU/100 mL is safe for swimming. Ta-An Beach in central Taiwan was found to have exceeded 1,000 CFU/100 mL, which is 51% of the total monitoring records. Sewage, piggery and duck wastewater are discharged directly into this area. The traditional pollution source trace methods did not clearly identify the pollution source. This study used PCR-DGGE technology to establish micro-organisms fingerprints from water samples using comparative analysis with microbiological composition, and then determined the possible sources of biological contamination. The E. coli colonies at all samples were processed using linear regression analysis and compared with each other. The R(2) is 0.4102-0.7387 for the livestock farm and beach. This shows a positively relation. The piggery impact is more obvious. The beach microbial communities exhibited high similarity with piggery wastewater from the upstream region. We confirmed that the major pollution source for Ta-An Beach comes from piggery wastewater. The proposed method has high stability and reliability. It can be used as the basis for rapid identification of pollution sources at other beach water sites in the future.