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The study presents the morpho-physiological performance under induced drought condition and molecular marker based genetic variability amongst 13 rice varieties released for cultivation in Uttar Pradesh, India. An attempt was made to identify suitable genotypes for drought affected areas, based on their morpho-physiological characteristics and genetic diversity. The physiological parameters of photosynthesis rate (A), transpiration rate (E), water use efficiency (WUE), along with the yield parameters and genetic diversity by simple sequence repeats marker (SSR) profile were analysed. The rice varieties PR-115 and PR-113 exhibited high water use efficiency, suggesting its possible advantageous response to drought due to low transpiration and high rate of net photosynthesis. The varieties, PR-115 and PR-113 were also found to be best performer in terms of yield under drought conditions. However, the more widely cultivated varieties namely Basmati, IR-36 and IR-20 were found to be intermediate in their response to drought for both yield and physiological parameters. The 19 simple sequence repeats marker (SSR) produces a total of 64 alleles across the 13 varieties, with alleles ranging from 2 to 7 per locus (average 3 alleles). The Polymorphic information content (PIC) value ranged from 0.13 to 0.78 with an average of 0.45 ± 0.19.