Knowledge of genetic diversity and relationship among breeding material at molecular level has significant impact on cotton improvement. In the present study genetic variability and relationships among six cotton genotypes, consisting three G. hirsutum varieties (G.Cot.16, G.Cot.20 and BC-68-2) and three G. barbadense varieties (Suvin, GSB-39 and GSB-41) were investigated using RAPD, ISSR and SSR markers. Twenty five RAPD, 19 ISSR and 26 SSR primers generated a total of 124, 65 and 71 alleles, of which 72, 45 and 59 alleles were found to be polymorphic, resulting in 58.06%, 69.23% and 83.09% polymorphism, respectively. The similarity coefficient based on RAPD, SSR and ISSR markers ranged from 0.57 to 0.81 with an average of 0.67, thus suggesting considerable genetic variation among the cotton genotypes studied. Further, dendrogram generated by UPGMA cluster analysis based on Jaccard's similarity coefficient, grouped six parental lines into two distinct clusters comprising of G. hirsutum varieties (cluster A) and G. barbadense varieties (cluster B). The grouping based on clustering analysis is in agreement with available pedigree, genetic background information and also confirms taxonomic classification. Our result suggests that combined molecular markers data are efficient for measuring genetic diversity and relatedness and also aid in selection of diverse outstanding lines to be used in future breeding programs to develop new cotton hybrids/cultivars.