The reducing cost of DNA sequencing and the increasing number of bacterial genome sequences have provided a chance to study the profile and evolution of microbial genome from population sight.Pan-genome, the genetic repertoire of a given species, comprises three parts including core genome, dispensable genome and strains-specific genome.Core genome represents those genes shared by all strains, and these genes are mainly responsible for basic process of life and species major traits.Dispensable genome includes those genes shared by two or more, but not all strains, and strains-specific genome are genes shared by only one strains.In general, dispensable genes and strain-specific genes function in contribute to the species diversity and selective advantages, such as adaptation to different niche and antibiotic resistance or colonization of a new host, and sometimes strains-specific genes are related to HGT.Since the pan-genome was present in Streptococcus agalactiae genome analysis for the first time, pan-genome analysis was employed in more than forty-three bacterial species or genus.Currently, the key issue for pangenome analysis is how to select appropriate mathematical models to depict the bacterial pan-genome feature and detect homologs (gene or genome region) from multiple genome sequences.Many algorithms and pipelines were designed to identify orthologs genes and homologs regions from multiple species, such as inparanoid/multiparanoid, Mauve, PGAP and so on.Species pan-genome profile was indicated from the relationship between the strains number and new detected genes, strains specific genes and the whole gene pool size under various mathematical models.Another important aspect is to combine specific problems in biology with pan-genome analysis.During these years, pan-genome analysis has shed a new sight into the dynamic variation of bacterial genes composition during differentiation and adaption to different niche, and facilitated the identification of strain-specific features, such as virulence genes, resistance gene and other genes function in extreme environment and special metabolic pathway.So, pan-genome has rather significant consequences for the way to study bacterial evolution, adaption and population structure, and it would be also helpful for controlling epidemic disease, developing vaccine, and enhancing the effect of industrial microbiology .