The present investigation was aimed at screening and analyzing 24 genotypes of Gossypium hirsutum (9 high oil percentages, 11 markers for internode length and 4 okra leaf structure) for assessing the link between the different accession of Gossypium hirsutum and to exploit the genetic diversity for future breeding programme. So, 20 random amplified polymorphic DNA (RAPD),19 inter simple sequence repeats (ISSR) and 14 simple sequence repeats (SSR) markers were used for determining polymorphism. The dendrogram generated showed similarity coefficient of 0.72 to 0.95 by RAPD markers, 0.76 to 0.95by ISSR marker and 0.77 to 0.98 by SSR marker. The average polymorphism detected by RAPD, ISSR and SSR were found to be 63.5 %, 55.1% and 55 % respectively indicating the importance of RAPD as a more informative primer than ISSR and SSR marker systems. The genotypes MAR-868, MAR-1297, MAR-1429 were identified as most diverse among all the cultivars studied which can be used in further breeding programmes. It indicated the importance of all the three marker system in the fast and reliable selection of the diverse genotypes for crop improvement in Gossypium hirsutum L.