Enterococcus faecalis (E. faecalis) is a homofermentative lactic acid bacterium widely used in food production. However， many E. faecalis strains are opportunistic pathogens， leading to significant controversy regarding their use in foods. This study focuses on dairy-derived isolates of E. faecalis to explore their safety. Using the Illumina HiSeq high-throughput sequencing platform， we performed whole-genome sequencing on 35 dairy-derived E. faecalis isolates and conducted comparative genomics analysis with 21 fecal isolates downloaded from the NCBI database. The results showed that the overall genome length of E. faecalis was (2.93±0.13) Mb， GC content was (37.43±0.13)%， the number of transfer RNA (tRNA) was 56±4， and the number of coding sequences (CDS) was 2 768±146. There was no significant difference in the average genome length of E. faecalis milk isolates from fecal isolates， but the average number of CDS was significantly higher than that of fecal isolates. The phylogenetic tree results showed that the strains of the same segregation were clustered in the same evolutionary branch， which was basically consistent with the average nucleotide identity (ANI) clustering results. Compared with fecal isolates， each strain contained 3 less drug resistance genes and 2.4 more mobile genetic elements. Therefore， even E. faecalis isolated from dairy products has a risk of pathogenic disease and needs to undergo strict safety evaluation before use.