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Drought is the most important constraint affecting production of chickpea and other crops as well. Quantitative traits like drought tolerance are multigenic and their inheritance is difficult to predict hence the need to explore more precise breeding techniques like maker assisted selection. The aim of this study was to introgress the identified root trait QTLs into Kenyan adapted cultivar to enhance drought tolerance through marker assisted backcrossing. Four varieties Chania Desi 1 (ICCV 97105), ICCV10, ICCV 92318, and Saina K1 (ICCV 95423) were selected as a recurrent parents for improvement among ten agronomically superior elite cultivars after exhibiting high polymorphism with SSR markers. Five molecular markers (CaM1903, CaM1502, TAA 170, NCPGR21 and GA11) were validated for use in MABC deployed in this study. Crosses were made between the four parents and ICC 4958 followed by marker screening of the F1 seedling progenies for the QTL of interest. Identified true heterozygotes were used as donors and backcrossed to the recurrent parent to obtain BC1F1 seeds. The process was repeated to obtain BC2F1 and finally BC3F1 with molecular marker identification of seedlings carrying the QTL region at each step. Results of evaluation in one trial site in Kenya semi-arid area (Koibatek ATC) of MABC lines for the four parents ICCV10 (24 lines), ICCV 92318 (8lines), ICCV 97105 (12 lines) and Saina K1-ICCV 95423 (10 lines) showed that the best progenies with higher levels of drought resistance and yield were ICCMABCD-21, 9, 20, 23, 15, 22, 5, 14, 16, 19 and 6 with yields > 2.5 tons/ha. The results indicated that it is possible to transfer QTL that confers drought tolerance using MABC. The best progenies are undergoing further evaluation to validate the contribution of the introgressed QTL in improving drought tolerance and yield.