Guinea pig as a commonly used laboratory animal is widely used in various fields of biomedical research. The stability of genetic quality directly affects its development and application. Genetic testing is designed to confirm the genetic characteristics of each strain, to verify whether there are genetic mutations and other genetic contamination, to ensure that the test object meets the requirements of this strain. Along with the emerge of biochemical and molecular marker technology, a more convenient and reliable means is provided for research of genetic homozygosity, genetic type detection and genetic quality monitoring of guinea pigs. In this paper, the application and research progress of biochemical, cytological and molecular markers in studies of guinea pig diversity will be summarized, and provide some help for genetic testing guinea pig.