Lactic acid bacteria （LAB） is one of the important industrial microorganisms. And LAB are also beneficial microorganisms in the intestine， which have the effect of improving the gastrointestinal environment and maintaining the balance of intestinal flora. The emergence of genome-wide association study （GWAS） provide more reliable degree of evidence and new ideas for the separation， traceability and evolutionary research for the LAB. This paper briefly describes the necessities of LAB molecular biology research， introduces the history of GWAS and the current situation of its application in bacteria， and looks forward to the application of this technology in LAB research， as well as the difficulties will be encountered in the future and solutions will be provided.