To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat(SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum×Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan(c M) of the cotton AD genome, with an average marker interval of 2.23 c M. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci(QTLs) for lint percentage(LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality. To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat (SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum × Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan (c M) of the cotton AD genome, with an average marker interval of 2.23 c M. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci (QTLs) for lint percentage (LP) were identified on nine chromosomes. Nine stable or Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07% -2.41%. These results indicated that the map could be used for screening for chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.