Using interval mapping and marker simple regression methods, the QTLs of yield and its components in (Simian 3 x TM-1) F2 and F2:3, were tagged and Mapped with 39 SSR and 10 RAPD markers having polymorphism between parents screened from 301 pair SSR primers and 1040 RAPD primers. Simian 3 is being grown extensively in Yangtze River cotton-growing valley characterized as high productivity with more bolls and higher lint percent, whereas TM-1, Genetic standard in Upland cotton with more heavy boll weight. In the present report, two QTLs controlling boll size with 18.2% and 21.0% phenotype variance explained in F2:3 generation, one QTL controlling lint percent with 24.9% phenotype variance explained in F2 generation and 5.9% in F2:3 generation and one QTL controlling 100-seed weight with 15.6% phenotype variance explained in F2:3 generation were mapped in Chromosome 9. Additionally, another QTL responsible for 100-seed weight was identified and mapped at the same position in Chromosome 9 in F2:3 generation. It is worth for further to be studied whether it is one QTL for pleiotrophism or two closely linked QTLs. The molecular markers mapped and tagged closely with main QTLs of yield traits in this paper can be used for MAS in cotton high-yield breeding program.