Pinus yunnanensis Franch. is an particular conifer tree species in Yunnan–Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were generally higher than that among populations in the most tested needle traits. The proportions of three-needle fascicle were significantly different among populations. The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio indices, including mesophyllarea/vascular bundle area, mesophyll area/resin canals area, vascular bundle area/resin canals area and mesophyll area/(resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596 % of the variation with eigenvalues [1; the differences among populations were mainly dependent on needle width,stomatal density, section areas of vascular bundle, total resin canals, and mesophyll, as well as area ratio traits.Seven populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, which would be helpful for management of genetic resources and reasonable utilization of them in future. Pinus yunnanensis Franch. Is an especially conifer tree species in Yunnan-Guizhou plateau in southwest China. The morphological and anatomical traits of needles are important to evaluate geographic variation and population dynamics of conifer species. Seedlings from seven populations of P. yunnanensis were analyzed, looking at 22 morphological and anatomical needle traits. The results showed that variations among and within populations were significantly different for all traits and the variance components within populations were higher than that among populations among the most tested needle traits. The proportions of three-needle The traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. Ratio traits related to needle size in both morphology and anatomy were positive with latitude and negative with annual temperature and precipitation. / resin canals area and mesophy ll area / (resin canals area and vascular bundle area), were negatively correlated with elevation and positively correlated with the annual mean temperature, showing some fitness feature for the populations. Needle traits were more significantly correlated with longitude than with other four environmental factors. Needle length was significantly correlated with almost all environmental factors. First four principal components accounted for 81.596% of the variation with eigenvalues ​​[1; the differences among populations were mainly dependent on needle width, stomatal density, section areas of vascular bundle, total resin canals , and mesophyll, as well as area ratio traits. Seive populations were divided into three categories by Euclidean distance. Variations in needle traits among the populations have shown systematic microevolution in terms of geographic impact on P. yunnanensis. This study would provide empirical data to characterize adaptation and genetic variation of P. yunnanensis, whi chwould be helpful for management of genetic resources and reasonable utilization of them in future.