Cowpea (Vigna unguiculata (L.) Walp.) is one of the most important foods and economic vegetable crops in the world. Plant breeders resorted to using mutagenesis, especially gamma radiation to improve the yield production and protein content. Two Egyptian cowpea varieties Dokii 331 and Kaha 1 were exposed to different doses of gamma rays (0, 50, 100, 150, 200, 250 and 300 Gy) to obtain mutations of economic value and to identify genetic variation by SCoT markers. The exposure of cowpea CVs. Dokii 331 and Kaha 1 to these gamma radiation doses had a positive effect on the early flowering, increase of the number of primary branches number of flowers per plant, pods per plant and the number of seeds, and consequently crop quantity. The dose of 150 Gy was effective in obtaining a dwarf mutation in cv. Kaha 1 where the length of the plant reached 33.4 cm. While in cv. Dokki 331, the dose of 250 Gy induced a change in size and pod color and increase number of pods per plant. While the effect of dose 300 Gy caused to change the color of flower from white to violet and plant length until it reached to 277.4 cm. However, the dose 300 Gy caused changing in the flower color and plant length reached 277.4 cm. Genetic variation in both irradiated cultivars was determined by SCoT markers analysis. The isolated DNAs from irradiated plants were amplified by fifteen SCoT primers. It was obtained 219 bands identified in both cultivars. Dakii 331 (105) Band was given by Polymorphic band number 46 (43.81%). Kaha 1 was 114 Band by Polymorphic band number 55(48.25%). Some SCoT primers were able to generate with a total of 26 specific markers. The cluster analysis based on Jacquard's similarity coefficients and UPGMA algorithms were calculated.

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