Abstract:In order to analyze the genetic variation and differentiation as well as the evolutionary history of Abies ziyuanensis, the nrDNA GapC gene intron sequences were used in this study. Eight polymorphic nucleotide sites and twelve haplotypes were detected from seventy alleles sequences of thirty-four samples from three A.ziyuanensis populations. Yinzhulaoshan (YZ), Dayuan (DY) and Shunhuangshan (SH) populations had ten, six and seven haplotypes, respectively. Seven individuals had more than two kinds of haplotypes. The haplotype diversity (h) of A.ziyuanensis was 0.817 0, ranging from 0.683 3 to 0.883 1 for different populations. The nucleotide diversity (π) of species and population was 0.003 90, ranging from 0.002 63 to 0.003 82. Research result of genetic differentiation (Gst=0.103, p<0.05) indicated that there was significant genetic differentiation among populations. AMOVA showed 88.64% (p<0.001) genetic variation within population and 11.36% (p<0.05) significantly genetic differentiation among populations. In Tajima’s D, Fu & Li’s D and Fu & Li’s Fs neutrality tests, the variation in nucleotides did not deviate from that expected with neutral evolution. There was no unique district branches in the gene genealogies of haplotypes. The result of mismatch distribution analysis showed no recent rapid expansion and no significant difference (p>0.05) between Nst(0.131) and Gst(0.103), which indicated no obvious geographic structure exists in A.ziyuanensis. We inferred that the extant A.ziyuanensis populations might be resulted from the habitat fragmentation in a relatively recent period.