The ability of Listeria monocytogenes to form biofilms is the key to its persistence in the food industry. Biofilm phenotype assessment is mainly based on physical and chemical methods, which are time-consuming. The aim of this study was to analyze genetic differences in the biofilm-forming ability of L. monocytogenes, found potential genetic markers, and quickly determined the biofilm phenotype. In particular, 103 strains of L. monocytogenes from agricultural products, were evaluated through multilocus sequence typing and their biofilm formation assays. The genetic characteristics of 12 representative strains were analyzed by comparative genomics, and the relevant genetic characteristics of the 103 strains were verified by polymerase chain reaction technology. The 103 strains were divided into 22 sequence types (STs), and top six types were ranked from high to low according to the median of biofilm biomass as follows: ST91, ST87, ST8, ST9, ST121, ST155, and all of them exhibited 2-3 biofilm phenotypes (strong, medium and weak). Comparative genomics analysis and verification identified the vip gene as a preliminary genetic marker for biofilm phenotypes, and the accuracy of determination can be improved by combining vip with 1-3 genes (srmB, cycB, and uvrB) or STs (ST8, ST87, and ST121). In addition, the smc_4, srmB-inlH, inlH and ssbA genes could accurately distinguish the phenotypes of ST9, ST155, ST91 and other STs. These genetic markers could be used as key targets for rapid determination of the biofilm phenotype of L. monocytogenes, thereby providing useful guidance for the optimization of disinfection processes in the food industry.