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Cluster bean, an important export commodity, is a drought tolerant crop of arid and semi-arid regions. This legume is not only grown for food, feed and fodder purpose but also having a vast range of diverse and unique industrial applications. Presence of galactomannan gum makes it an important industrial crop with commercial outlook. Owing to its high industrial qualities, there is a requirement for well documentation to increase cluster bean production. In this study the genetic/diversity was assessed among 31 cluster bean genotypes using morpho-physiological, yield and SSR markers. A total of 17 morphological traits were studied for the analysis of variance, correlation and path coefficient. The genotypes showed considerable amount of variability for most of the traits with high heritability (>51%). All the genotypes were classified into five groups on the basis of standardized morphological data. SSR amplification with 17 primers detected 33 alleles with a mean of 1.83 alleles/SSR. The clustering revealed five distinct groups at 0.68 cut-off value. The cluster analysis showed low genetic variation among the genotypes studied. The phenotype-based cluster did not correspond with the molecular-based cluster as the correlation coefficient for the two clustering matrices was negative (r = -0.72). The results of the present study indicated that molecular markers as a complementary tool should be used in conjunction with morphological characterization for better description of the level and pattern of genetic diversity, and for crop improvement. (C) 2016 Elsevier B.V. All rights reserved.