Cotton scientifically known as Gossypium hirsutum L. is a dwarf plant from the Malvaceae family and from the Gossypeae clan, that is native to tropical and subtropical regions. Cotton is one of the most important sources of oils globally and is rich in fiber and protein. It can also be used as animal feed. The purpose of this study was to compare the primary and secondary metabolites of the seed of two species, G. hirsutum L. and G. arboreum L. Compounds such as flavonoids, alkaloids, tannins, saponins, and steroids were detected in the two types of cotton. The biochemical properties of gossypol, flavonoid, flavonol, phenol and the antioxidant capacity of the cotton-seeds were evaluated. The results of the study indicated that G. arboreum L. as compared to G. hirsutum L. is valuable for use as animal feed and oil extraction, due to its higher amounts of fat, fiber and protein. A comparative study of the two species showed that both species had high antioxidant capacity and gossypol levels. Type G. hirsutum L. has greater quantities of phenol and flavonol than G. arboreum L. which can lead to the use of this species for breeding purposes and the creation of resistant strains to biological stress. The presence of large amounts of gossypol in the studied species indicates that consideration should be given for their utilization in various applications in the food and feed industry.