Cotton fiber strength is mainly determined during the secondary cell wall (SCW) thickening stage. In 24―25 days post anthesis (DPA) of SCW thickening stage, cDNA-amplified fragment length polymorphism (AFLP) was carried out to construct fiber transcriptome groups. Based on these groups, cotton fiber strength candidate genes were detected by composite interval mapping (CIM) through quantitative trait locus (QTL) scanning. The mapping population was the interspecific backcross BC1 of Gossypium hirsutum × G. barbadense. One hundred and fifteen BC1 plants were used for group construction with 102 qualified absence/presence polymorphic transcript-derived fragments (TDFs) from G. barbadense, and 78 TDFs were assigned into eight transcriptome groups that gave a total length of 462.63 centimorgans (cM). Two significant QTLs, FS1 and FS2, were detected and explained 16.08% and 15.87% of fiber strength variance, respectively. Of the six TDFs co-segregating with FS1 and FS2, except one encoding an unknown protein, five targeted putative phosphatidylinositol kinase, trehalose-6 phosphate synthase, MADS transcription factor, cellulose synthase-like protein and phenylalanine ammonia lyase, respectively. These functional genes were involved in plant cell wall morphogenesis or cellulose synthesis metabolism processes, and were considered as the candidate genes controlling cotton fiber strength. In 24-25 days post anthesis (DPA) of SCW thickening stage, cDNA-amplified fragment length polymorphism (AFLP) was carried out to construct fiber transcriptome groups. Based on these groups, cotton fiber strength candidate genes were detected by composite interval mapping (CIM) through quantitative trait locus (QTL) scanning. The mapping population was the interspecific back cross BC1 of Gossypium hirsutum × G. barbadense. One hundred and fifteen BC1 plants were used for group construction with 102 qualified absence / presence polymorphic transcript-derived fragments (TDFs) from G. barbadense, and 78 TDFs were assigned into eight transcriptome groups that gave a total length of 462.63 centimorgans (cM). Two significant QTLs, FS1 and FS2, were detected and explained 16.08% and 15.87% of fiber strength variance, respectively. Of the six TDFs co-segregating with FS1 and FS2, except one encodin g an unknown protein, five targeted putative phosphatidylinositol kinase, trehalose-6 phosphate synthase, respectively, MADS transcription factor, cellulose synthase-like protein and phenylalanine ammonia lyase, respectively. These functional genes were involved in plant cell wall morphogenesis or cellulose synthesis metabolism processes, and were considered as the candidate genes controlling cotton fiber strength.