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Most of the modern-day improved watermelon varieties succumb to various biotic and abiotic stresses mainly because of their narrow genetic base. Insights into the genetic diversity and population structure are crucial for broadening the genetic base and improving the adaptive value. The present experiment was conducted to study the genetic diversity and population structure of a germplasm panel comprising 336 Citrullus sp. accessions. Another objective was to formulate a core collection of Indian Citrullus sp. accessions. Data from 23 highly polymorphic microsatellite markers were used for genetic diversity and population structure analysis while both molecular and phenotypic data from 17 traits were used to formulate the core set. The markers yielded a total of 69 alleles with an average of three alleles per locus. Initially, the accessions clustered into two populations and an admixture group. Intra-population analysis revealed three and two statistically distinct subpopulations in Pop I and Pop II, respectively. The exotic collections were predominant in Pop I-A, Pop II-A and Pop II-B while the Indian accessions were preponderant in Pop I-B and Pop I-C. Pop I-B recorded the maximum magnitude of gene diversity and the highest number of alleles. The well-adapted Indian landraces could be deployed in future watermelon improvement programmes. The formulated core collection (n = 46; 23.71% of the entire collection studied) would ease in maintenance of the diversity present among indigenous Citrullus sp. accessions; would ease trait search while exploring Indian diversity and can be pooled with other collection(s) to form a global core of watermelon. [ABSTRACT FROM AUTHOR]