Abstract: In the past 30 years, the investigation of ancient DNA has been vigorously developed. Under the background that highthroughput sequencing technology is widely employed, the ancient DNA plays an important role in clarifying the mechanism of origin, domestication, evolution and phylogenetic reconstruction of plants and animals. In this paper, the research progress on application of high throughput sequencing technology in investigation of ancient DNA was reviewed, the existing problems in study of ancient DNA were summarized, and the development of ancient DNA study in future was prospected.