| Abies ziyuanensis, wihch is a rare and endangered species, is a member of Pinaceae family. Being the state-protected and first-class endangered species, A.ziyuanensis mainly distributed in the mountainous areas such as Yinzhulaoshan of Guangxi, Shunhuangshan and Dayuan of Hu'nan and Jinggangshan of Jiangxi. Survived the Quaternary glaciation stage, A. ziyuanensis is very important for studying the ancient climate and geography in the south of China. The distributional pattern of A.ziyuanensis is like a block and the population size is small. RAPD, ISSR and AFLP markers were employed to assess the genetic diversity in the A. ziyuanensis with a sample of 139 individuals from seven populations. The conclusions of study on A. ziyuanensis by three molecular markers thereinafter:Firstly, low genetic diversity of A. ziyuanensis is revealed based on RAPD and ISSR, while the higher one based on AFLP compared with the formers. The average percentage of polymorphic bands (PPL) is 68.06% for RAPD, 63.38% for ISSR and 83.55% for AFLP respectively. The Nei's genetic diversity index (He) is 0.1862 for RAPD, 0.1527 for ISSR and 0.2595 for AFLP respectively. The Shannon diversity information index (I) is 0.2870 for RAPD, 0.2349 for ISSR and 0.3969 for AFLP respectively.Secondly, a high degree of genetic differentiation among populations of A.ziyuanensis is found by Nei's and AMOVA analysis. Genetic variation is detected among populations (Gst is 0.4202 for RAPD,0.5159 for ISSR and 0.4822 for AFLP). The gene flow (Nm) is estimated to be 0.5575 of seven populations, 1.0725 of populations distributed in Yinzhulaoshan and Shunhuangshan, and 0.6129 of populations distributed in Dayuan. Genetic differentiation has already existed between distribution regions and among populations. Furthermore, there is significant correlation between genetic distance and geographical distance(r=0.8440, p=0.01). The genetic structure of natural populations might affected by the disturbance of gene flow...
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