Abstract: The polymorphism and cluster analysis based on genetic similarity matrices of SSR markers were used to identify three groups of isogenic lines genetically distinct in fiber development. The three groups of isogenic mutants includes: (1) fuzzless-lint mutant GZNn, GZnn, n2, fuzzed-lint line NN2-2 and the upland cotton genetic standard line TM-1; (2) fuzzless-lintless mutant XZ142w and its wild type XZ142. (3) fuzzless-lintless mutant Xinxiang xiaojie wuxu (Xin) which maybe derived from CCRI No.12 or Yumian No.4. SSR markers and morphologic analysis indicated that the mutant fuzzless-lintless Xin maybe the mutant of Yumian No.4. The molecular marker analysis indicated that the mutant XZ142w possessed lots of mutant genes and genetic differences compared with that of the wild type. .Moreover, the results of research showed that the polymorphic SSR primers can groupe the mutants with similar phenotypes together. This indicated that the variability of germplasm phenotypes accorded with the cluster analysis of SSR markers. Therefore, SSR marker technology is one kind of effective techniques for analysis germplasm genetic differences and biodiversity.

Key words: Naked seed cotton, SSR marker, Fingerprint atlas, Clustering analysis