Germplasm resources are rich and the species and the varieties are wide in Paeonia L., which is of important ornamental and medicinal value. This paper systematically discusses the research advances in genetic diversity of Paeonia Sect. Moutan DC and Sect. Paeonia, which contain relatively rich germplasm resources from the level of DNA molecular. It was suggested that different provenances were the main factor contributing to the genetic differences in Paeonia; genetic diversity had a great correlation with flower color, flower type and plant height only on the premise of consistent provenance. All the research results were widely different by molecular markers and DNA sequence analysis, but it could be sure that dividing Sect. Moutan into two subsections was perfectly reasonable; most researchers paid more attention to P. suffruticosa than to P. lactiflora, as a result, research activities on genetic diversity in Sect. Paeonia were still not deep\|going enough. Henceforth, we must utilize comprehensively various genetic markers and sequence analysis to accelerate the development of whole genome sequences in Paeonia, and further the exploration and application of all kinds of new marker methods. Meantime, the advance research direction of genetic diversity in Paeonia was presented, which will undoubtedly provide scientific references and information on the conservation and utilization of Paeonia resources.