Watermelon belongs to the genus Citrullus. There have been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in Citrullus is still limited. The present study was conducted in 2012–13, to evaluate the genetic diversity and population structure of the 1197 line watermelon collection maintained by the Beijing Vegetable Research Center (BVRC), which belongs to seven Citrullus species including Citrullus naudinianus, Citrullus colocynthis, Citrullus rehmii, Citrullus ecirrhosus, Citrullus amarus, Citrullus mucosospermus, and Cirullus lanatus subsp. vulgaris. Twenty-three highly informative microsatellite markers evenly distributed in the watermelon genome were used to assess genetic diversity in this collection. The markers detected on an average of 6.05 alleles per locus with the average value of polymorphism information content (PIC) at 0.49. A high level of gene diversity [Nei’s gene diversity index (Nei) = 0.56] and a low observed heterozygosity (Ho = 0.10) were revealed within the collection. Structure analysis grouped the 1197 accessions into two main populations (Pop I and Pop II) and an admixture group. Pop I contained 450 accessions from C. lanatus subsp. vulgaris (446) and C. mucosospermus (4). Pop II comprised 465 accessions, 379 of which belonged to C. lanatus subsp. vulgaris and 86 to C. naudinianus (3), C. ecirrhosus (2), C. rehmii (2), C. colocynthis (11), C. amarus (58), and C. mucosospermus (10). The remaining 282 accessions were classified as an admixture group. The two main populations were further subdivided into four subgroups. The groupings were consistent with the estimation of F statistics (Fst) and Nei’s genetic distances in collections. We confirmed the distinct genetic backgrounds between American and East Asian ecotypes. Subsequently, we defined a core set consisting of 130 accessions including 47 from Pop I, 68 from Pop II, and 15 from the Admixture group. This core set was able to capture all 133 alleles detected by 23 simple sequence repeats (SSRs) in 1197 accessions. These results will facilitate efficient use of genetic variations in Citrullus in watermelon breeding and help optimization of accessions in genomewide association studies.

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