Due to increasing population growth and anthropogenic pollution in the coastal zone, contamination of water and seafood with pathogens is probably responsible for the greatest number of human morbidities and mortalities worldwide. Hence, regular monitoring of waterborne pathogens is required to safeguard public health. Current techniques rely on the culturing of nonpathogenic indicator organisms (e.g. Escherichia coli or coliforms) for detection by inference. However, recent epidemiological evidence shows poor correlation between concentrations of E. coli/coliform and waterborne pathogens. Moreover, traditional methods are slow, not cost-effective, unable to distinguish harmful from benign strains, and fail to detect viable but nonculturable pathogens. The use of the polymerase chain reaction (PCR) has provided rapid and highly sensitive methods for the specific detection of pathogenic microorganisms. This paper briefly reviews some DNA-based technologies for waterborne pathogen detection, and describes our recent development of two new DNA-based technologiesdquantitative multiplex PCR (Q-mPCR) and DNA microarraydthat allow simultaneous and cost-effective detection and quantification of numerous pathogens in a single sample, which is superior to the culture methods currently in use.