This paper presents several common molecular typing methods, Pulsed-Field Gel Electrophoresis (PFGE), Restriction Fragment Length Polymorphisma (RFLP), Random Amplified Polymorphic DNA (RAPD), Automatic Ribotyping, rep-PCR, Multi-Locus Sequence Typing (MLST), in which the application and progress of molecular typing of pathgens for these methods are described. These methods played an important role in pathgens source tracking, knowing the source(s) of bacteria in pharmaceutical, preventing and controlling the diarrhea and food-poisoning outbreaks, which have great value in the remediation and prevention of further bacterial contamination.