Abstract: AFLP variation of 164 individuals of eight natural populations of Psilopeganum sinense,an endemic and rare plant of Central China,was analyzed to investigate the genetic variation and genetic structure of the species.A moderate low genetic diversity was observed in the species and average variation of populations significantly lower than the variation of species level.A relatively low level of genetic diversity was observed in the species,and the genetic diversity within populations was significantly lower than that within the species.Five AFLP primers produced 180 bands,of which 76 were polymorphic,accouting for 42.2%.The percentage of polymorphic bands of eight natural populations was 3.3%-16.7%,respectively,with an average percentage of 9.4%.The Nei’s gene diversity of eight natural populations was 0.01987-0.06987 and the Shannon’s Information Index was 0.0197-0.0816.Average of Nei’s gene diversity was 0.03420,and average of Shannon’s Information Index was 0.0510.They were all lower than the average of species of the world level,but were higher than the average of the endemic species level.The average of Nei’s gene diversity and Shannon’s Information Index was 0.03420 and 0.0510 respectively,which were lower than the average of species in the world level but higher than the average of endemic species.In addition,Gst was 0.5069,which indicated that high population differentiation occurred.Analysis of molecular variance(AMOVA) of 164 individual revealed that 13.17% genetic variation was among the populations of four geographical regions and 50.45% genetic variation among the populations within the four regions;and 36.38% of total variance was distributed within populations.Nm was 0.2432,which implied that the gene flow was not enough to maintain gene exchange and current genetic structure.The result of UPGMA cluster showed that eight natural populations were genetically clustered in two groups,of which one was Yanduhe population and the other included the remaining seven populations.Mantel analysis of NTSYS indicated that genetic divergence was not correlated with geographical distance.At last,we analyzed the cause why P.sinense was endangered,and we concluded two main factors as follows.One was low genetic diversity that maybe due to bottleneck effect,inbreeding depression and the absent of natural selection,the other cause of population decline of P.sinense appeared to be from human disturbance.In correspondent with this,we proposed some effective strategies to conserve the species.