With the development of genome sequencing and the accumulation of whole genome sequences, genome-wide association study (GWAS) has achieved remarkable advances in understanding of human complex disease, and tens of thousands of disease risk factors have been found. Meanwhile, GWAS provides a new tool for exploring the genetic mechanism of bacterial phenotypes. Since the publication of the first bacterial GWAS (BGWAS) work in 2013, there have been more than 10 reports, which reveal the genetic basis of host adaption, drug resistance and virulence, etc. These findings greatly enhance our understanding on genetics, evolution and spread of bacteria. In this review, we summarize the current methodologies, applications and problems of BGWAS and highlight its potential in future research, which aims to provide helps for the applications of BGWAS in the field of microbiology.