Vancomycin functionalized silver nanorod arrays substrates were used to obtain the surface enhanced Raman scattering (SERS) signals of six foodborne pathogenic bacteria in mung bean sprouts samples using both a portable and a handheld Raman system. The silver nanorod arrays substrates were optimized to facilitate quantitative, rapid, and sensitive detection of Salmonella enterica serotype Anatum, Salmonella enterica serotype Cubana, Salmonella enterica serotype Stanley, Salmonella enteritidis, Escherichia coli O157:H7, and Staphylococcus epidermidis. Substrate optimization was achieved by varying the nanorod length and vancomycin incubation concentration. By combining these substrates with a two-step filtration process we found that the foodborne pathogenic bacteria used in this study can be identified in mung bean sprouts with a limit of detection as low as 100 CFU ml(-1) in less than 4 h using both portable and handheld Raman systems. The results show that SERS spectra can be used to differentiate between bacterial species and serotypes when chemometric methods are employed. The low detection limit and rapid detection time of this biosensing platform for foodborne pathogenic bacteria could be a valuable field detection method for the fresh produce and food processing industries.