The genetic diversity of 5 populations of Paeonia decomposita and 4 populations of Paeonia decomposita subsp. rotundiloba was dectected by intersimple sequence repeat markers(ISSR). (1) For P. decomposita, the percentage of polymorphic loci(PPB) at the species level, Neis gene diversity(H) and Shannons information index(I) were 89.36%, 0.291 4, 0.441 3, respectively, while for P. decomposita subsp. rotundiloba, the three indices were 81.91%, 0.285 7, 0.428 5, respectively, all lower than that of P. decompositas. The genetic variation of them were little lower at population level. (2) The coefficient of genetic differentiation among population(G_st) was 0.355 5 for P. decomposita and 0.379 1 for P. decomposita subsp. rotundiloba, suggesting that for both species there is a high genetic differention within population; the gene flow of the two species was 0.906 5 and 0.819 0, respectively and show that gene flow was limited among populations. (3) Mantel test indicated that there was a significant correlation between genetic and geographic distances among P. decomposita populations, whereas no significant correlation between genetic and geographic distances of P. decomposita subsp. rotundiloba populations. (4) UPGMA analysis showed significant genetic differention between the two species at molecular level, supporting the view that they are two separate species. The study indicated that P. decomposita suffered human disturbance and natural disaster may be its endangered reasons. P. decomposita subsp. rotundiloba populations are subjected to severe disruption as well, even more serious than P. decomposita populations. So all the individuals of populations should be protected in situ timely, and it is as large as possible to gain the sample in order to reserve their genetic diversity owning to the genetic variation mainly exist in population.