E. coli in seawater can be simply and efficiently detected by direct PCR. The sensitivity of detection is significantly improved using magnetic beads based bacterial pre-concentration. abstract Foodborne and waterborne E. coli remains a major economic burden worldwide. Assaying seawater for trace levels of E. coli is challenging since it applies time-consuming preparations, expensive instrumentation and complicated procedures. Therefore, there is a continued demand for new analytical technologies that can detect low bacterial concentrations in a more cost- and time-effective manner. In this study, combination of E. coli pre-concentration with a direct polymerase chain reaction (PCR) was shown to enable rapid bacterial detection without enrichment step or DNA extraction/purification. The E1 aptamer that targets E. coli surface epitope grafted onto magnetic beads efficiently concentrated E. coli from water samples containing high concentration of NaCl. When direct PCR was performed on bacteria attached to these aptamer-modified magnetic beads, a limit of 10(3) CFU/mL was obtained. The overall analysis was performed in less than 3 h. This approach may lead to a future PCR-based biosensor system for online monitoring of enteric bacteria in seawater.