A backcrossed inbred line (BIL) population has been devloped from a cross between Upland and Pima cotton and phenotyped in 2005 and 2006. To identify functional markers associated with fiber yield and quality traits, cDNA-AFLP analysis has been performed to identify polymorphic gene markers that segregate in the BIL population. More than 100 polymorphic cDNA-AFLP markers were cloned and sequenced, some of which are homologous to genes with known or predicted functions and are associated with fiber traits. The cDNA-AFLP has also been used to construct cDNA libraries for Pima, Acala and Upland cotton for gene seuqencing. A pilot test has demonstrated the success of this strategy for developing SNP markers.