Farmers in outlying locations who are short on resources often rely on banana production, but this fruit crop is in danger due to drought. Given the difficulties of banana breeding, a molecular understanding of banana's drought tolerance will be invaluable in identifying markers for use in marker-assisted selection and genes for transgenic improvement of drought tolerance. The purpose of this study was to identify the genes and expression markers in banana that confer resistance to drought. Under the greenhouse, both dessert and cooking bananas were grown under ideal and water-restricted conditions and looked at how drought affected the biochemistry, structure, and function of these plants. The cooking cultivar is drought tolerant because it may reduce water loss by partially closing its stomata, as shown by morphological and physiological studies. The stomatal conductance, relative water content, plant height and number of leaves were significantly reduced in both the genotypes under water deficit stress. It was also discovered that MaADH, MaDEH19, MaNAC, MaSPS, and MaWRKY had higher expression levels in samples under water deficit stress when compared to the well watered samples. The expression of genes MaAQP, MaStpkNAK and MaRAV were found to be down regulated under water deficit stress in the drought tolerant cultivar Monthan. However, the expression of MaEXP and MaStpkNAK was non significant in the drought susceptible cultivar Amritsagar under water deficit stress. Present study finds out that MaEXP was exclusively upregulated in the drought tolerant cultivar Monthan under water deficit stress. However, its expression was non-significant in the susceptible cultivar under same condition. It is also revealed that under non stress conditions, MaAQP was upregulated in the drought tolerant cultivar as against to that of susceptible one, however, imposing water deficit stress will downregulate the gene in the tolerant cultivar. The current work proposes that cellular tolerance is founded on differences in the transcript levels of certain genes involved in processes like water transport and osmotic adjustment.