In this paper, the surface-enhanced Raman scattering (SERS) is used as an analytical tool for the detection and identification of pathogenic bacteria of Escherichia coli (E. coli) and Salmonella typhimurium (S. typhimurium). Compared with normal Raman signal, the intensity of SERS signal is greatly enhanced. After processing all SERS data, the obvious differences between the SERS spectra of two species are determined. And applying the chemometric tools of principal component analysis and hierarchical cluster analysis (PCA-HCA), the SERS spectra of two species are distinguished more accurately. The results indicate that SERS analysis can provide a rapid and sensitive method for the detection of pathogenic bacteria.