Abstract: To study the accuracy of identification and correlation analysis of microbial taxonomy for enterobacteriaceae by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method, it was adopted to conduct protein mass spectrum collection on 10 species of enterobacteriaceae isolated from the surface of kumquat, and microorganism identification and phylogenetic analysis were achieved by comparing the characteristic peaks of mass spectrum. And in the meanwhile, 10 species of enterobacteriaceae were extracted and sequenced by 16SrDNA to get the identification on the level of molecular biochemistry, in addition, phylogenetic tree analysis of 16SrDNA sequences was realized by Neighbor-joining. The identification results of enterobacteriaceae based on MALDI-TOF MS and 16SrDNA were identical for 8 of 10 species of enterobacteriaceae, but the identification of two Klebsiella spp. differed on species level. The data resulted from MALDI-TOF MS and 16SrDNA can be used to evaluate the correlation of microorganisms and obtain the phylogenetic tree, on which the positions and directions of microorganisms that belong to one genus were the same, but enterobacteriaceae that belong to different genus had comparatively large disparity on the related distances and positions. MALDI-TOF MS is rapid and accurate for the identification of microorganisms on the surface of agricultural products, however, to establish phylogenetic correlation, it is necessary to expand the database and optimize algorithms.