In that DNA diversity detected nowadays could not mean phenotypic diversity,it is the precondition of breeding project and basic research of crop improvement that genetic diversity analysis and sampling of core collection by phenotypes.Phenotyping and statistic analysis on 9 traits of 92 accessions of cotton germplasm resource from three species（Gossypium hirsutum L.,Gossypium barbadence L.and Gossypium arboreum L.）were conducted.And the statistics（variation coefficient,proportion of special accessions and Shannon-Weaver information index）indicated that initial collection had abundant phenotypic diversity;software NTSYS-pc and the unweighted pair group method of arithmetic（UPGMA）were used for the cluster analysis on genetic similarity coefficient and genetic distance matrix,and the result showed that the genetic relationship among accessions was highly consistent with the pedigree;22 accessions of core collection were selected by software QGAStation,four statistics,such as variance difference percentage（VD%）,mean difference percentage（MD%）,coincidence rate（CR%）and variable rate（VR%）,showed that the genetic diversity of core collection was approximately equal to the initial collection.The results of genetic diversity analysis based on phenotypic data and sampling of core collection would provide reference for breeding projects and basic research.
