A mentotaxus yunnanensis Li(Taxaceae)is a rare and relict species with limited distribution．RAPD markers were used to determine the genetic variation within and among 4 populations of A.yunnanensis and one population of A. formosana. Although high level ofgenetic diversity was found in A. yunnanensis at the species level(Percentage of polymorphic loci：79.0％，Nei’S genetic diversity：0.2718)，there existed much lower genetic variation within populations(Percentage of polymorphic loci：18.0％ and 6.9％：Nei’s genetic diversity：0.0688 and 0.0198，for A. yunnanensis and A. formosana. respectively)．A high degree of diferentiation among populations was detected in A．yunnanensis(0.76ll，0.7503 and 0.7526 for AMOVA，Nei’S coefficient of diferentiation(GST) and Shannon inform ation index，respectively)．It is suggested that the historical factors，including severe bottleneck and subsequent genetic drift during Quatemary glaciations and fragmentation in postglaciation，small population sizeandlow seedling establishment would have contributed to such a population genetic structure in A．yunrumensis．Based on these results，strategies are proposed for the genetic conservation and management of A．yunnanensis