Abstract: In this study, seven traits of ten bundle needles of each trees collected from 18 populations of Pinus yunnanensis in main distribution regions were measured. The results showed that there were significant differences both among populations and within populations in each needle trait, which suggested that there existed wide and abundant genetic variation in Pyunnanensis populations. There were different variation tendency of each needle trait among populations. The phenotypic variation was more abundant within population than among populations. The coefficients of variation (CV) were lower than 50%. There were weak phenotypic differentiation or no phenotypic differentiation for each pairwise population based on individual needle trait. Different needle traits revealed the genetic relationship among populations in varying degrees. The complex of the measured needle traits could reflect the genetic relationship among populations. The test on geographical and ecological distance with relations of genetic distance of each trait indicated that was no obvious effect of isolation by distance (IBD) and isolation of ecology (IBE) in needle trait, but the effect of IBE was more obvious than IBD. The phenotypic differentiation among populations may be influenced by the complex of the geographical, climatic and soil factors. Cluster analysis indicated that each popolation was not clustered entirely based on geographical distribution.