Abstract Totally 13 natural populations of Pinus bungeana were collected. Five characteristics, including seed length (SL), seed width (SW), cone length (FL), cone width (FW) and weight (WT) of 1000 seeds, were measured. The variance analysis of the five characteristics showed that there were significant differences among populations with the F value from 2.44 to 14.68, and there were also significant differences among families within a population with the F value from 7.48 to 44.53. The variance factors analysis indicated that the variation within a population was the main part of the phenotypic variation in Pinus bungeana, which stood four out of totally five, but the phenotypic differentiation among populations were very obvious ( VST =22.8%), which meant that there was a strong adaptability to environment pressure in Ｐinus bungeana . The variation coefficients ( CV ) and relative extreme value ( Ri ′) within each population show similar tendency. Based on Duncan's Multi comparison analysis, all the 13 populations were divided into four groups. The populations in groups A and B have higher phenotypic diversity while the populations in group C and group D have lower phenotypic diversity. Seed characteristics display a significant ecological gradient variation. There is close relationship between phenotypic diversity of seeds and economic characteristics of progeny.