Salmonella is an important foodborne pathogenic bacterium, with more than 2 500 serotypes. A number of techniques have been developed for Salmonella subtyping, including phenotypic and genotypic techniques. Traditionally, Salmonella isolates are identified and typed by phenotypic techniques such as serotyping and phage typing. During the last two decades, genotypic techniques have been used for differentiation of Salmonella isolates and source tracing of foodborne outbreaks. These methods include molecular serotyping, pulsed field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), multi-locus variable number of tandem repeats analysis (MLVA), and clustered regularly interspaced short palindromic repeats (CRISPR). Compared with phenotypic methods, genotypic methods are widely applied for Salmonella typing due to their high discriminatory power and good reproducibility. Molecular serotyping, as a new method, is to identify serotypes of Salmonella by PCR. PFGE is considered the “gold standard” for Salmonella subtyping. MLST and MLVA, as DNA sequencing-based methods, are publicly available online and can be compared readily between laboratories. CRISPR typing has a high distinguish capacity among the same serotype with homology and satisfying genotyping result. However, each typing method has different advantages and drawbacks, operating conditions, and applicability. Therefore, it is necessary to choose the suitable typing methods for genetic diversity analysis according to the characteristic of strains and experimental facilities available.