The genus Dipteronia Oliv.endemic to central and southern China consists of two species,D.sinensis Oliv.and D.dyeriana Henry,both of them are rare and endangered.In this study,a combination of 18 random amplified polymorphic DNA(RAPD) markers,8 pair of amplified-fragment length polymorphism(AFLP) primers and 10 polymorphic chloroplast microsatellite loci(cpSSR) were used to access the genetic diversity and population structure of species D.sinensis and D.dyeriana.At the species level,the genetic diversity estimated by the two nuclear markers RAPD(D.sinensis:H=0.386 4,H_sh=0.556 3 and D.dyeriana:H=0.304 7,H_sh=0.445 0) and AFLP(D.sinensis:H=0.331 9,H_sh=0.488 0 and D.dyeriana:H=0.304 7,H_sh=0.445 0) were comparable,while that of cpSSR(H_e=0.603 2 of D.sinensis and H_e=0.671 1 of D.dyeriana) were much higher than that of both AFLP and RAPD,and the gene differentiation coefficient(G_ST) displayed a similar trend.The resulting values indicated that the three marker types estimated a relative high genetic diversity and genetic differentiation within both species.For the implication of conservation,we believe that the habitat destruction by human activities is among the key factors responsible for both species’ endangered status.Therefore,in the long term,the strategy for conservation of the two Dipteronia species is the protection of its habitat.In addition,increasing small population size to maintain existing levels of genetic variation should be taken into consideration.