Chickpeas are a global crop supplying cheap protein and other nutrition. Inducing genetic variability is an essential step in any plant breeding program. This study investigated the direct and indirect effects of various gamma doses (0, 100, 200, 300, and 400 Gy) on seed yield and other quantitative traits in two chickpea genotypes, Kabuli (Giza 531) and Desi (Giza 3) for two subsequent (M1 and M2) generations. Non-significant differences were found in the number and percentage of germinations between the irradiated and control seeds. The G.3 variety recorded more pods and seeds, while G.531 excelled in seed yield and pod weight. The most significant response appeared at 200 Gy, with a reduction at 300 Gy and the most severe response at 400 Gy. The number and percentage of survival plants showed highly significant variances in both seasons, which ranked at 60% for 200 Gy, then 56% for control, followed by 100 Gy (48%), 300 Gy (41%), and 400 Gy (24%). Various levels of polymorphism were displayed by molecular markers, with SCoT at 85.05% and SRAP at 70.59%. Polymorphism information, marker index, effective multiplex ratio, and resolved power parameters were computed to assess the effectiveness of the markers. Gamma rays induce wide genetic variability at phenotypic and genotypic levels in chickpeas. The Kabuli genotype (G.531) generally has a more significant response to gamma-used doses than the Desi genotypes (G.3). These findings can guide plant breeders in determining the appropriate gamma dose to enhance chickpea seed yield, warranting further research.