Conventional plate counting with selective agars is time-consuming and labor intensive for the detection and enumeration of microorganisms associated with food-borne illnesses from food and environmental samples. In addition, it may be unsuitable for the rapid estimations required for food sanitation and hygiene. To overcome these technical challenges, a superior method, termed FISHFC (fluorescence in situ hybridization [FISH] in combination with filter cultivation [FC] on a membrane filter), was developed. The FISHFC method has equal detection accuracy to the conventional plate counting method. It enumerates only viable food-borne pathogens from food samples within 8-17 h, which suggests that the accurate evaluation of pathogen contamination can be completed within two working days. Therefore, the FISHFC method with species-specific detection probes contributes to ensuring food safety. This article introduces the rapid enumeration FISHFC method for the estimation of food-borne pathogens.