Abstract: A total of 4961 pairs of different sources SSR primers were used to screen polymorphism between two parents, 71 pairs of them with stable amplification and clear bands were used to amplify among the 261 F2 and resulted into 71 polymorphism loci. With the Joinmap 3.0 software with LOD of 3.0, a total of 49 loci was grouped into 14 linkage groups and covered 498.7cM, approximately 10.0% of the total recombinational length of the cotton genome. 13 groups have been anchored to the chromosomes. A total of 11 stable QTLs, 2 for boll weight, 4 for lint percentage and 5 for fiber quality including 2 for fiber uniform, 2 for micronaire and 1 for fiber elongation, were detected in F2 population of CCRI48. By Complex Interval Mapping (CIM) method with the software of Win QTL Cartographer 2.5. These stable QTLs with greater phenotypic variations could be used for maker assisted selection for yield and fiber quality.and be used as molecular marker assisted breeding.