Salmonella and Staphylococcus aureus are prevalent in food and environment， and pose certain threats to food safety. During foodborne pathogens identification， appropriate identification method choosing can shorten time， save manpower and material resource， increase the trace ability. In this study， 210 Salmonella and 18 Staphylococcus aureus strains acquired in our previous study were further identified using 16S rDNA sequencing， MALDI-TOF-MS and VITEK automatic microbiological identification system. Identification level and efficiency of each method and the correlation among the identification results were statistically analyzed using R software（v3.6.1）. The results indicated 210（100.0%） Salmonella strains could be identified into genus level via the 3 methods， 18 （100.0%） Staphylococcus aureus strains could be identified into species level by any of MALDI-TOF-MS and VITEK. When 16S rDNA sequencing method was used， 18 （100.0%） Staphylococcus aureus could be identified to genus level， and 15 （83.3%） strains could be identified into species level. In addition to 16S rDNA sequencing method， the other 2 methods had the same identification ability for Staphylococcus aureus and Salmonella， however， time usage of MALDI-TOF-MS was the shortest.