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Not AvailableHigh-isoflavones soybean genotypes are desired in nutraceutical industry. Conversely, low-isoflavones soybean genotypes are preferred to regular soybean in designing soy-based infant formula and in developing soy food products with reduced astringent taste. Concentration of individual form of isoflavones viz. daidzein, glycitein and genistein was determined in the seeds of 46 Indian and exotic soybean genotypes using high performance liquid chromatography. The study exhibited a 9-fold (234.3-2092.5 µg/g of seed) genetic variation for total isoflavones content, with 19 genotypes falling in high isoflavones (>1200 µg/g), and 14 genotypes in low isoflavoes category (<600 µg/g). For developing genotypes with further high or low values of isoflavones, it is critical to hybridize genetically diverse parents with-in high or low-isoflavones genotypes as analysed by HPLC. Genetic diversity analysis carried out using 58 simple sequence (SSR) markers exhibited 144 alleles with polymorphic information content (PIC) varying from 0.00 to 0.773. The pair-wise genetic similarity value between soybean genotypes varied from 0.24 to 0.95. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) allocated the genotypes in 5 clusters with fairly good bootstrap support. Mantel’s test for cophenetic correlation with r = 0.810 indicated a good fit of the soybean genotypes in a group in the cluster analysis. Genetically diverse parents identified in low- and high-isoflavones category can be crossed to obtain trangressive segregants.Not Availabl