Seeds from different indigenous watermelons were analysed for their chemical composition such as phenolics, proteins, oils, minerals, ash and fibre content as well as antioxidant activity measured in methanol extract using 2.2-diphenyl-1-picrylhydrazyl (DPPH) assay. The morphological variations of watermelons, which revealed diversity in terms of fruit and seed colour were also assessed. Average percentages for lipid content, total proteins, crude fibre, ash and total carbohydrates as 34.4, 16.5, 23.1, 3.99, and 3.16%, respectively, were recorded for Capricorn district and 31.6, 14.9, 22.0, 4.58, and 5.26% were recorded for Sekhukhune landraces. The Capricorn landraces had higher content of flavonoids (0.222 mg/g) than Sekhukhune varieties (0.130 mg/g). But, landraces from Sekhukhune had higher antioxidant activity (46.5%) which corresponded to higher total phenolic content of 0.59 mg/g. Thus, suggest that watermelon seeds may serve as potential source of natural products for food, feed and pharmaceutical applications.