In order to investigate the pattern of fruit phenotypic trait variation in natural population of Phyllanthus emblica among populations and variation within populations，eight morphological traits in six P.emblica populations in Yunnan have been measured.The variance analysis of the eight characteristics showed that:(1)There were partly significant differences among populations with F value from 20.17 to 35.21,and there were very significant differences families within a population the F value from 1.27 to 3.07.(2)The variance factors analysis indicated that the variation within a population was the main part of the phenotypic variation in P.emblica which stood nine out of totally ten.(3)The phenotypic traits of P.emblica change in the ecological and geographical factors were significantly associated.Principal component analysis showed that single fruit weight,fruit horizontal diameter,epicarp weight,stone width,stone heavy were the most important phenotypic traits that accounted for the fruit morphological variation of P.emblica.