Abstract: We analyzed the genetic diversity of 6 natural populations of Abies chensiensis (120 individuals) based on 10 simple sequence repeat markers to clarify genetic diversity, genetic structure and changes in gene flow in the populations. We detected 149 alleles in 10 microsatellite loci; the mean number of alleles per locus (A) was 14.9; the effective number of alleles per locus (Ne) was 7.7; the mean expected heterozygosity (He) was 0.841; and the mean observed heterozygosities per locus (Ho) was 0.243. The Shannon diversity index (I) was 2.13, with the proportion of genetic differentiation among populations (F_ST) 6.7%. Gene flow between the populations (N_m) was 3.45. We found no significant correlation between genetic distance and geographic distance (r=0.490 6, P>0.05). Genetic diversity in the natural population of A. chensiensis was relatively low, with genetic variation mainly among populations. Our results, a field survey and related literature suggest that the gene flow between natural populations in A. chensiensis is higher than before, with perhaps distant hybridization between populations.