Watermelon is an important cucurbit grown throughout the world. The crop is cultivated in areas with hot, humid climate with extended frost-free months. The crop was first domesticated in Africa over 4000 years ago and most likely spread from Africa to the Middle East, Asia, China, and America. There exists a huge genetic variability in qualitative and quantitative traits in watermelon. The narrow genetic base of cultivated dessert types is one of the major challenges in watermelon improvement. Many cultivars have been developed and commercialized all over the world and most of them with a common genetic background. The land races and semidomesticated wild relatives are available and least characterized in watermelon. These could be a reservoir of genes for many important traits and could be utilized for enriching the genetic diversity in this crop, particularly with emerging threats of biotic and abiotic stresses. Watermelon’s genome has 424 million base pairs. The smaller genome made this crop suitable for genetic studies. Several international research agencies maintain a large number of watermelon germplasm, including the related Citrullus spp., and developed a number of trait-specific germplasm, including lines resistant to multiple stresses. Here, we reviewed the important genetic resources available and its utilization in trait-specific improvement in watermelon.