Livestock feces and domestic sewage are the one of the main factors inducing water pollution, while the identification of the pollution source is particularly important in pollution control and management. Because of this, microbial source tracking (MST) has recently been paid more and more attention by the related researchers around the world. In this paper, the research progress of two types of MST methods, their advantages and disadvantages, and existing problems in application were reviewed and discussed. It was considered that in the library- and culture-dependent MST methods, PCR genotyping based on repetitive sequences was most practicable, while in the library- and culture-independent MST methods, PCR-DGGE based on the gene of specificity in Escherichia coli had a very glaring sight. Future researches should be more focused on the library- and culture-independent MST, and the combination of library- and culture-dependent MST with library- and culture-independent MST could make the tracking results more credible.