Abstract: Inter-simple sequence repeat (ISSR) marker technology has become a hotspot in DNA molecular technology in recent years, and plays an important role in genetic research. However, this technology is still at an initial stage in animal research, compared with its applications in plant research. This paper introduced the principles and main methods of ISSR marker technology, and summarized its applications in analyzing the genetic structure of animals, such as genetic diversity, resources identification, and genetic relationship, etc. The application prospects of this technology were also discussed, aimed to provide reference for the further applications of this technology in animal research.