Splice variants have major impact in plant response to drought stress. Alternative splicing a major post-transcriptional modification and its differential sensitivity to drought stress is of paramount importance to resolve complex molecular response of drought stress and to develop drought-resilient crops. In the present study, we analyzed the alternative splicing pattern of drought-tolerant (DT) and -sensitive banana (DS) cultivars under drought conditions and found that the number of spliced transcripts in DS (AAA genome) has increased to about 4.32 folds, while 0.19 fold among all the splicing events were reduced in DT (ABB genome). Categorization of drought -modulated alternative splicing (AS) events revealed that intron retention is the most abundant (42.5%) process, followed by alternative splice acceptor (22.6%), alternative splice donor (12.2%), and exon skipping (4.86%) in DS. Only 40-44% of intron retained transcripts have the protein coding capacity, indicating that their occurrence would participate in drought stress response as modified yet functional proteins. We observed that retained introns were slightly higher in GC content than constitutively spliced introns. The results reveal that the genotype dependent AS pattern may play an important role in drought tolerance in banana. This study will help in deciphering the molecular basis underlying phenotypic differences among tolerant and sensitive banana cultivars.