Bacteroidales has been proposed as a fecal pollution indicator. microbial source tracking (MST) based on Bacteroidales host-specific gene markers has recently been applied in the fecal pollution identification, which does not require culturing the fecal pollution indicator organisms. This method needs to design specific primers. The primers are designed based on Bacteroidales specific 16S rRNA gene. Once a pair of specific primers was amplified, the fecal pollution can be identified. In this paper, the progress of specific primers of Bacteroidales in human, swine, ruminant feces were reviewed and discussed. The advantages and disadvantages were put forward. Future researchers should be focused on the new biological markers and the combination of different MST methods.