Genetic diversity of 45 Chinese Sea Island Cottons and 8 foreign Sea Island Cottons were studied based on SSR (Simple Sequence Repeats ) markers.Twenty-four SSR primers were selected from 256 primers to evaluate the genetic diversity of 53 Gossypium barbadense L. germplasms. Totally 106 alleles were observed among which, 97 (91.5%) were polymorphic. The number of DNA bands per primer ranged from 2 to 8 and with the average of 4.4. The average polymorphism information (PIC) was 0.688,with the range from 0.245 to 0.848. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that 53 varieties were clustered into 2 main groups based on Jaccard similarity from the SSRs and Euclid distance from 17 agronomic traits data. Classification of all genotypes gave similar results with their line sources. Genetic relationships and the genetic similarity obtained from the analysis is used for the evaluation of varieties and genetic diversity.