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As a kind of important lactic acid bacteria,Enterococcus is widely used in fermented food.However,as some strains of Enterococcus are opportunistic pathogen,its safetY has not been generally accepted,so there are many restrictions in the use of Enterococcus in food industry.At the same time,the comparative genomic analysis of the genus Enterococcus is relatively late.In order to further understand the genetic relationship and the evolution of genus Enterococcus,the comparative genomic analysis was used in this study.The genomes of 29 type strains of Enterococcus were sequenced by the Illumina Miseq high-throughput sequencing platform.In combination with 8 complete genome sequences,the whole genomes of 37 strains of Enterococcus were comparatively analyzed.The core-genomes which contains 605 genes were defined based on the genomes of the 37 strains of Enterococcus.The core genes were mainly associated with carbohydrate metabolism,protein metabolism,DNA and RNA metabolism.The phylogenetic tree of 37 strains of Enterococcus was constructed based on core-genome sequences and the 37 strains were divided into 8 branches.Six out of 7 strains isolated from plants and birds are in the ancient branches.And all 19 strains isolated from human and mammals distribute in the young branches.At the same time,compared with the old branches,the structure of young branches is more complicated.This may be due to the environment.As human and mammal habitats are more suitable for the evolution of Enterococcus,so the evolution rate is faster in the human and mammal isolates than that in plant and birds isolates,so all the human and mammal isolates were distributed in the young branches.Furthermore,the comparative genomic method was used to study the function of genes in different species.The functional genes related to carbohydrate metabolism,stress response system,virulence factors and antibiotic resistance were discussed detailed.