A full-length cDNA clone with high homology with Brassica napus peptide methionine sulfoxide reductase (PMSR) gene (BnPMSR), which could reverse oxidation of methionine residues into MetSO in protein, was cloned by suppression subtraction hybridization and cDNA library screening from Gossypium barbadense. This gene (named as cMsrA; Accession number: AY224208) had a total length of 1059 bp with an open reading frame of 765 bp, and encoded a predicted polypeptide of 255 amino acids with a molecular weight of 28.4 kDa. The cMsrA protein shared 68.6, 66.3 and 65.8% identity with those PMSR proteins isolated from B. napus, A. thaliana and L. sativa respectively. Expression patterns revealed that cMsrA was enriched later and weaker in resistant variety 7124 (Gossypium barbadense) than sensitive variety Ejing-1 (G. hirsutum) under salt treatment and pathogens attack. These results indicated that cMsrA played an important role in protecting the cells against oxidative damage during the pathogens and salt stress.