Cotton seeds oils have their potential biological activity and specific physicochemical properties, due to which they are playing vital role in human nutritional diet for health benefits. The aim of this study was to compare secondary metabolites, physicochemical properties and fatty acids composition of seeds oil extracts of Gossypium hirsutum L. and Gossypium barbadense L. Cotton seeds used in this study were obtained from the Agricultural Research and Technology Corporation (ARTC), Wad Medani, Sudan. Seed oils methanolic extracts of Gossypium hirsutum and Gossypium barbadense were screened for their accumulated secondary compounds. Results indicated that G. hirsutum seed oil has more alkaloid than G. barbadense, whereas no variation in the amount of saponins, tannins, phenolic compounds, flavonoids and steroids & terpenoids in two mentioned species. Physicochemical properties analyses were carried out using standard analytical methods. Results of physical properties showed that the specific gravity and refractive index@25C0 were 6.73 and 1.470 for G. hirsutum compared to 6.87 and 1.475 for G. barbadense respectively. Density (g/c3) of seed oils in order were 0.935 and 0.939 whereas pH was 6.76 and 5.76. The chemical properties of oils of two studied species recorded acid values (mg KOH/ g), % of free fatty acids, peroxide values (meq/Kg fat), saponification value (mg KOH/g) and iodine value (I/g oil) were in order 7.1and 20.3; 3.3and 10.3; 0.00 and 0.00; 188.0 and 195.0; 113.6 and 110.4 for G. hirsutum and G. barbadense respectively. Fatty acids composition of seed oils of two species were revealed using the gas chromatography-mass spectrometry (GC-MS) technique. The dominant unsaturated fatty acids of G. hirsutum seed oils were oleic acid 13.11% and linoleic acid 44.25%, while the saturated fatty acids were palmitic acid 29.16 %, methyl stearate acid (stearic acid) 5.06%, methyl tetradecanoate (methyl myristate) 1.48% and arachidic acid 0.67%. Comparatively, the unsaturated fatty acids of G. barbadense were oleic acid 22.63 % and linoleic acid 9.65 %, whereas the saturated fatty acids were palmitic acid 40.12%, methyl stearate (stearic acid) 7.18%, methyl tetradecanote (methyl myristate) 1,71% and arachidic acid 1.51%. In conclusion, the study revealed that oils extracted from G. hirsutum and G. barbadense, grown in Sudan contain the main saturated and unsaturated fatty acids. Physicochemical properties showed standard values in most parameters especially for G. hirsutum. Secondary metabolites obtained indicated the presence of biological activities in the oils of these species.