Abstract:12 phenotypic traits from leaves,fruits and seeds were investigated for 210 individuals in 7 natural populations of Diospyros glaucifolia from south-east China and the relationship between phenotypic variation of the natural populations and different distribution areas was discussed using variance analysis and nested variance analysis. The relationship among phenotypic variation of the natural populations, geo-ecological factors and morohlogical traits was discussed by correlation analysis. The results showed that there were significant differences in phenotypic variation among and within populations. It also showed that the diversity within populations was higher than that among populations. The average differentiation coefficient of seed traits is the smallest in all phenotypic traits.The traits stability of seeds was higher than that of other traits. There was no significant relationship between traits. The traits variation of natural populations were affected mainly by longitude (such as LL and LW) and height(such as seeds weight) in spatial distribution. The 7 populations investigated could be divided into five groups according to the cluster analysis.