Abstract:The geographical isolations in the Qinghai-Tibetan Plateau region were suggested to have played an important role in the high diversification of plants occurring there. It remains elusive whether this mechanism had also contributed to the morphological differentiation and the following speciation of the wind-pollinated conifers. In this study, we investigated the within-specific diversity and phylogenetic relationships of different variants within Picea likiangensis, a dominant forest species in this region based on random amplify polymorphism (RAPD) markers. Our results suggested that this species has a high overall genetic diversity with mean percentage of polymorphic loci at p=85.42%. Consistent with the initial expectation, a high level of genetic differentiation among populations was detected based on Nei’s genetic diversity (Gst=0.256) and AMOVA analysis (Phist=0.236). However, gene flow among populations are limited (Nm=1.453 2), far lower than reported for other conifers with the wide distribution ranges from the other regions. Three morphological variants respectively in the south, the north and the west show no corresponding clusters according to UPGMA analyses. However, this clustering pattern further suggests multiple origins of the north variants from the south one. It is a probable scenario if considering that more than one of refugia probably existed for this species in the south during the glacial stages and that the postglacial recolonizations from different refugia toward the north occurred. The intra-specific morphological differentiation in this species might reflect the ecological adaptation to the current environmental gradients.