Abstract: Objective To develop two rapid assays to detect three emerging pathogens (O139 Vibrio cholerae, EHECO157 ∶ H7, Listeria monocytogenes)by using immunomagnetic separation (IMS). Methods Two assays of IMS-Ch and IMS-PCR were established in combination with chromogenic media (Ch) and quantitative fluorescencet PCR. The sensitivity and specificity of two assays were compared and the evaluation on the effectiveness on the detections of high risk samples was conducted. Results IMS-Ch could detect the samples containing 50 cfu/10 g pathogen in 24 hours and the detection threshold of IMS-PCR to EHEC O157 ∶ H7 and Vibrio cholerae was 10-20 cfu/10 g in 9 hours. The Youdens index of this assay was more than 95%. Conclusion IMS-PCR is a reliable and rapid screening assay, IMS-Ch is a more sensitive and rapid confirmation assay.