Pinus yunnanensis Franch. is a major component of coniferous forests in southwestern China. Little is known about its intraspecific variation. Morphological variations in needle and cone traits of P. yunnanensis were analyzed to quantify variability among and within natural populations.Seven traits were measured on 10 needles collected from 30 trees in each of the 18 sampled populations of P. yunnanensis. Four cone traits were measured in 221 individual trees from nine populations. The results showed that there were significant differences(p 0.01) both among populations and within populations in each needle and cone trait.The proportion of phenotypic variation of nearly all needle and cone traits was over 50 % within populations, which showed trees within populations accounted for a majority of the total variation. The needle traits showed higher variability within population than cone traits. Variability in theneedle traits was correlated with geo-climatic parameters(longitude, latitude, altitude, temperature, and precipitation).Needle length and the ratio of needle length to fascicle sheath length showed clinal variation in response to latitudinal and altitudinal gradients. A hierarchical classification of all populations based on needle traits led to the formation of four major groups. The findings provide important genetic information for the evaluation of variation. Moreover, it will assist in management of genetic diversity of P. yunnanensis. Pinus yunnanensis Franch. Is a major component of coniferous forests in southwestern China. Little is known about its intraspecific variation. Morphological variations in needle and cone traits of P. yunnanensis were analyzed to quantify variability among and within natural populations. Nine needles collected from 30 trees in each of the 18 selected populations of P. yunnanensis. Four cone traits were measured in 221 individual trees from nine populations. The results showed that there were significant differences (p 0.01) both among populations and within populations in each needle and cone trait. the proportion of phenotypic variation of nearly all needle and cone traits was over nearly 50% within populations, which showed trees within populations accounted for a majority of the total variation. cone traits. Variability in theneedle traits was correlated with geo-climatic parameters (longitude, lat itude, altitude, temperature, and precipitation) .Needle length and the ratio of needle length to fascicle sheath length showed clinal variation in response to latitudinal and altitudinal gradients. A hierarchical classification of all populations based on needle traits led to the formation of four major groups. The findings provide important genetic information for the evaluation of variation. it, it will assist in management of genetic diversity of P. yunnanensis.