Abstract: Abstract: The G. hirsutum ZMS36 and the G. barbadense Hai1 were crossed to construct backcross populations (BC1F1, BC2F1, and BC1S1) with ZMS36 as recurrent parent. A total of 2102 pairs of SSR primer were used to screen polymorphism among the parents ZMS36, Hai 1 and their F1, which resulted in 317 pairs of polymorphic primer with the special band for Hai 1, and the polymorphism primer accounted for 15.08% of the total primer, and 275 of them were used to screen the BC1F1 population. Linkage test（LOD=6.5）indicated 254 of 306 polymorphic locus derived from 275 pairs of primer could be mapped into 42 linkage groups and covered a total genetic distance of 2252.36cM, approximately 50.05% of cotton genome. The number of the marker locus per linkage group was 6.08, which spanned 53.63cM of the cotton genome. And the average distance of the neighboring marker locus were 8.87cM. 16 QTLs for yield-related traits were detected from the three generations of BC1F1, BC2F1, and BC1S1 using CIM. QTL numbers for lint percentage, boll weight and seed index were 6, 6 and 4, respectively, which accounted for 5.77%～19.86% of phenotypic variance. Among the 16 QTLs, 9 with positive additive effect derived from ZMS36 and 7 QTLs with negative additive effect from Hai1, which indicates the materials with poor phenotypic characteristics may contain the useful gene for improving the same traits. 3 QTLs for lint percentage could be stably detected in the different generations, and from high-value parent of ZMS36, which should be useful for the marker-assisted selection.