Genetic diversity among 65 selected genotypes of Gossypium arboreum race bengalense was explored using 62 simple sequence repeats (SSR) and 73 interspersed sequence repeats (ISSR) markers. The SSR primers produced a total of 170 alleles (all polymorphic), while ISSRs yielded 281 bands of which only 94.3% were polymorphic. Utility of various markers were evaluated by calculating different parameters like polymorphic information content (PIC), marker index (MI), and discriminative ability (D), on

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... the basis of which 21 SSR and 53 ISSRs primers were found very efficient for genetic diversity analysis. ISSR outperformed the SSR for discriminative ability as it yielded higher number of banding patterns (ISSR-658, SSR-175), greater numbers of polymorphic bands/assay (ISSR-3.63 and SSR-2.7) and higher D values (ISSR-0.862 and SSR-0.442). Values of I (SSR-0.740 and ISSR-0.421) and He (SSR-0.433 and ISSR-0.262) indicated SSRs as more suitable for characterizing the species in terms of abundance and evenness of alleles. A slight difference was observed in terms of MI values of the SSR (1.20) and ISSR (MI-1.38), showing an edge for ISSR in detecting overall polymorphism among given genotypes. Phylogenetic analysis was carried out by SSR, ISSR as well as combined datasets of markers. The highest value of cophenetic correlation coefficient was obtained for ISSR (r=0.94), followed by combined datasets (r=0.91) and SSR markers (r=0.87).