Among the OPM primers, OPM-17 did not give amplification, whereas the primers 01, 02, 03, 05, 08, 13, 14, and 15 did not show any polymorphism among the samples. Amongst the polymorphic OPM primers, the OPM-4, OPM11 and OPM-19 confirmed the introgression of DNA fragments of sizes, 750 bp, 1 kb and 750 by bands respectively of G. arboreum into G. hirsutum on molecular level. Whereas none of the 20 OPM primers showed polymorphism even between G. hirsutum and G. barbadense parents. Out of 12 OPB primers two primers OPB-3 and OPB-4 were found to be polymorphic between G. hirsutum and G. barbadense parents while 6 OPB primers (OPB-05, 06, 07, 08, 11 and 12) showed polymorphism between G. hirsutum and G.arboreum parents. However these polymorphic OPB primers could not detect polymorphism between parents and their transformed progenies. Therefore these studies have confirmed the introgression of G. arboreum DNA fragments into G.hirsutum through DNA macroinjection via DNA mediated embryo transformation technique.