Drought stress has become a significant abiotic stress for wheat in Bangladesh. This study aimed to explore drought tolerance in Bangladeshi wheat based on morpho-physiological and molecular traits. Ten wheat genotypes selected based on the previous research were grown in pots under control (100% field capacity) and drought stress (30% field capacity), applied from third leaf stage till maturity. Drought stress affected the yield contributing characters and significantly reduced grain yield. Drought susceptibility index and drought tolerance efficiency were used as criteria for selection. Sonalika, Sourav, and BARI gom-28 were least affected and emerged as drought tolerant. Durum, Pavon-76, BARI gom-25, and BARI gom-33 were moderately tolerant, while BARI gom-24, BINA gom-1, and BARI gom-20 were susceptible as they were severely affected. Thirteen SSR markers linked to drought tolerance were used to characterize 26 wheat genotypes. A total of 73 alleles were detected with an average of 5.62 alleles per locus. Polymorphism information content (PIC) and Nei’s (Proc Natl Acad Sci USA 70:3321–3323; 1973) gene diversity were 0.69 and 0.73, respectively. The coefficient of genetic similarity matrix for all 325 pairs of genotypes ranged from 0.15 to 1.00 with an average of 0.57. Similarity indices-based cluster analysis separated 26 genotypes into different groups. Two tolerant genotypes, Sourav and Sonalika, and two moderately tolerant genotypes, Durum and Pavon-76, as identified by morphological study were grouped in cluster 1. These four genotypes, therefore, passed the screening for drought tolerance in molecular and morphological studies and are promising for cultivation in the drought-prone areas of Bangladesh.