[Background] Enterococcus faecalis, as an important lactic acid bacteria, is widely used in dairy products and pharmacy. However, many E. faecalis isolates are opportunistic pathogen. So it is important to analyze of virulence genes in E. faecalis. [Objective] To study the virulence genes of E. faecalis from different environments and evaluate the safety of E. faecalis isolated from naturally fermented dairy products. [Methods] Comparative genomic analysis was used to determine the virulence genes of 107 strains isolated from dairy products, blood, urine, feces and water. Principal component analysis (PCA) was used to compare the virulence genes of different isolates. The habitat-specific virulence genes were screened by Pearson’s chi-squared test. [Results] A total of 88 virulence genes were identified in 107 genomes of E. faecalis isolates. These virulence genes were mainly involved in adhesion. There was no significant difference in the number of virulence genes between dairy isolates and the other isolates. [Conclusion] The results indicated that the E. faecalis isolated from dairy products were also at risk of pathogenicity. The safety of E. faecalis must be evaluated before using in the food industry.