Abstract: The genetic relationship and genetic diversity of 56 Sea-island cotton (Gossypium barbadense L.) were analyzed by 95 pairs of SSR markers. Among the 56 Sea-island cotton varieties,33 of which come from former USSR,1 from USA,1 from Albania,9 from Xinjiang and seven respectively come s from Yunnan, Jiangsu , and other places of China. Among the 95 pairs of polymorphic SSR primers 384 alleles were amplified in total ,and 296 were polymorphic, which accounted for 77.1% .2 t o 9 alleles could be produced from each pair of primers with average of 4.1.The gene diversity (H) was 0.035 to2.931 with average of 0.879. Shannon's information index（I）was 0.09 to 4.417with average of 1.363.The trend of each index is accordant. The value of allelic polymorphism information content (PIC) ranged from 0.035 to 0. 926,on an average of 0.698 per SSR marker. The genetic similarity of paired varieties ranged from 0.585 to 0.952,with average of 0.7,and the genetic similarity of 97% tested materials ranged from 0.6 to 0.8.which showed a high genetic similarity. The result of UPGMA cluster showed that four groups could be clearly clustered when genetic similarity coefficient was given as 0.69.The first ? group contained 27 varieties . mainly from former USSR. But Giza 77 ,Paizi cotton and zhong 239 were assigned ? to this group.The second group was a little complicated and mostly included 6 varieties from Xingjiang and 4 ? varieties from Egypt . The third group contained 8 varieties and 6 of them were from former USSR but 3116 from Xinjiang and JI B91-45 from Hebei.were also clustered in this group. The last group contained only one variety L-8007 from former USSR. Our result showed again as a kind of codominant markers ,SSR can be used for the pedigree analysis and identification of Sea-Island especially.Therefor SSR markers proved to be the work of Sea-Island cotton breeding practice of matching parents, to provide a reliable basis for the molecular level.