Taxus chinensis and T. wallichiana in have been threatened in their distribution areas in recent decades because of their over-exploitation and reduction and destruction of native habitats. Determining the genetic diversity in populations of the two species will provide guidelines for their protection and preservation. Two hundred and fifteen trees from six populations of T. chinensis and150 sampled trees of T. wallichiana were sampled. Six microsatellite primer pairs selected from 16 primer pairs were used to investigate genetic variation at the population and species levels. Five yielded polymorphic alleles, and among the 13 putative alleles amplified, 11 were polymorphic(accounting for 76.33 %).Shannon’s information index(I) and percentage of polymorphic bands(PPB)(I = 0.202 and PPB = 67.22 % for T. chinensis; I = 0.217 and PPB = 65.03 % for T. wallichiana). Both species had low levels of genetic diversity(mean H_o= 0.107, H_e= 0.121 for T. chinensis; H_o= 0.095, H_e= 0.109 for T. wallichiana). Genetic differentiation among populations was higher(FST= 0.189) for T. chinensis and lower(0.156) for T.wallichiana, indicating limited gene flow(Nm) among populations for T. chinensis(0.68) and T. wallichiana(0.65).Variation among individuals of T. chinensis was 63.59 and73.12 % for T. wallichiana. Thus, the threatened status of the two conifers is related to a lack of genetic diversity. All populations are isolated in small forest remnants. An ex situ conservation site should be established with a new population for these species that comprises all the genetic groups for the best chance to improve their fitness under environmental stresses. Taxus chinensis and T. wallichiana in have been threatened in their distribution areas in recent decades because of their over-exploitation and reduction and destruction of native habitats. Determining the genetic diversity in populations of the two species will provide guidelines for their protection and preservation. Two hundred and fifteen trees from six populations of T. chinensis and 150 sampled trees of T. wallichiana were sampled. Six microsatellite primer pairs selected from 16 primer pairs were used to investigate genetic variation at the population and species levels. Five yielded polymorphic alleles, and Shannon’s information index (I) and percentage of polymorphic bands (PPB) (I = 0.202 and PPB = 67.22% for T. chinensis; I = 0.217 and PPB = 65.03% for T. wallichiana). Both species had low levels of genetic diversity (mean H_o = 0.107, H_e = 0.121 for T. chinensis; H_o = 0.095, H_e = 0.109 for T. w (0.68) and T. wallichiana (0.65) for T. chinensis and lower (0.156) for T. wallichiana, indicating limited gene flow (Nm) among populations for T. chinensis .Variation among individuals of T. chinensis was 63.59 and 73.12% for T. wallichiana. Thus, the threatened status of the two conifers is related to a lack of genetic diversity. All populations are isolated in small forest remnants. An ex situ conservation site should be established with a new population for these species that all all the genetic groups for the best chance to improve their fitness under environmental stresses.