Fecal microbial contamination in the food chain is a significant concern in the field of food safety as it is one of the most important pathways causing foodborne diseases. Microbial source tracking (MST) is an effective approach to address this issue, which can track the sources and contamination of fecal microbes. MST methods can be categorized into two types: library-dependent methods (LDMs) and library-independent methods (LIMs), with LIMs including culturedependent and culture-independent methods. The non-culture-dependent method using 16S rRNA and host-microbial interaction genes as specific molecular markers has been widely used to investigate microbial contamination in the food chain. This review provides an overview of the basic principle and characteristics of MST, and focuses on recent advances in MST methods based on host-specific molecular markers for tracing microbial contamination in the food chain. Furthermore, future prospects of MST are discussed based on its unique advantages and disadvantages.