Cowpea is a leguminous crop that has received widespread attention due to its high nutritional value. However, it is prone to losing some of its nutritional content due to the long cooking process. In this study, fourteen cowpea genotypes were evaluated for their chemical properties before and after cooking, along with the effect of different cooking treatments on the cooking time, considered as the main indicator of the cooking quality. Moreover, the correlation between molecular markers (simple sequence repeat (SSR) and intersimple sequence repeat (ISSR)) and the cooking time of cowpea genotypes was determined. The obtained results showed significant differences between all the investigated genotypes before and after the cooking procedure, reflecting significant genotypic and heritability estimates. Kareem 7 and Greenish Black Balady genotypes showed the shortest cooking time. Microwave's treatment manifested the shortest cooking time compared with the other treatments, which appeared as a new approach to improve the cooking quality of cowpea seeds. Spearman's rank correlation showed that the calculated values were smaller than the tabulated value at 0.05, reflecting the existence of a rank correlation between SSR/ ISSR- PCR banding products and the cooking time of cowpea genotypes. Such a study appeared to be a new approach, particularly in Egypt for the proper selection of the optimal cowpea seed on the basis of its cooking quality.