Cre/loxP system is composed of Cre recombinase and loxP site. Cre recombinase can recognize loxP site and catalyze precise site-specific recombination of DNA between two loxP sites. The Cre/loxP system can modificate the genes in specific time and site, which acts in simple mode and recombinates in high efficiency. It has become an important tool for experiments that can be used to change the genetic information directionally in vivo. In this article, the structure, the mechanism of the recombination, the characteristics of Cre/loxP system and its application in the field of oral medicine have mainly been reviewed.