Ta-an Beach in Taichung County, central Taiwan, was found to have exceeded 1,000 CFU/100 ml, 51% of the total monitoring records. It is difficult to identify the contamination source using traditional Escherichia coli and Enterococci analysis. Therefore, a more advanced method known as molecular biotechnology is adopted in this study to diagnose the sources of E. coli at Ta-An Beach. After comparing several different groups of micro-organisms in water samples, we know that there are E. coli and Bacillus. This shows that the beach water quality is indeed affected by contamination from land drainage, and the numbers of E. coli and non-E. coli coliform in land drainage is far greater than that normally found at the beach. The analytical methods and techniques used in this study were not significantly different from the results detected using standard data analysis. The proposed method has high stability and reliability, providing ways to track and identify future of contamination.