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In a first report, watermelon (Citrullus lanatus) landraces from diversity rich Indo-Gangetic plains and arid regions of India were characterised using watermelon specific SSR markers. Thirty eight landraces were compared with germplasm of diverse origin comprising of cultivars, landraces and wild types. Significant differences were observed for days to first fruit maturity, average fruit weight, fruit number, total fruit yield, TSS and lycopene content. Thirty three polymorphic SSRs generated 120 bands with a mean of 3.63 per marker. Average PIC value was 0.46. Observed heterozygosity (0.50) was more than expected heterozygosity (0.45). Neighbour joining tree based on SSR analysis grouped accessions into seven clusters. Wild types formed a distinct cluster. Landraces showed genetic intermediateness with both the wild and cultivated watermelons. Combined morphological and molecular analysis revealed modern cultivars from USA, China, Japan and South Korea genetically resembled with each other. Hybridisation between landraces and exotic cultivars can be exploited to expand the genetic variability and introduce new traits in the breeding programs. (C) 2017 Elsevier B.V. All rights reserved.