Horizontal gene transfer (HGT) plays an important role in the evolution of bacteria. HGT occurs mainly through three mechanisms: transduction which is mediated by bacterial phage, conjugation and natural transformation. Natural transformation is the process by which natural competent bacteria can take up DNA from the environment and integrate it into their own genomes. Natural transformation was first found in Streptococcus pneumoniae in 1928. Until now, at least 83 bacterial species have been found to be natural competent. Among them, the natural transformation mechanism of Gram-positive bacteria Streptococcus pneumoniae and Gram-negative bacteria Neisseria were studied well, respectively. The biological functions of natural transformation have been hypothesized as follows: obtaining nutrition, repairing DNA damage, and biological evolution. However, there are still debates on this. In this paper, it will describe the molecular mechanism of bacterial natural transformation in details, and discuss the biological function of natural transformation. It will be helpful to further understand the bacterial natural transformation.