Background <p>Drought stress significantly hinders the growth and productivity of many crops, including lentil. Hence, improving our understanding of the genetic and molecular bases underlying drought response is essential for mitigating yield losses under water-limited conditions. The primary objective of this study was to identify quantitative trait loci (QTLs) associated with various morpho-physiological traits using genotyping-by-sequencing (GBS) and to identify putative candidate genes contributing to drought tolerance in lentil.</p> Result <p>A F₇ recombinant inbred line (RIL) population was developed to map QTLs for morpho-physiological traits including root and shoot length, fresh and dry weight of roots and shoots, drought score, seedling survivability, relative water content, proline, superoxide dismutase (SOD), glutathione peroxidase (GPX) enzyme activities and seed yield/plant under controlled (hydroponic) and rainout shelter conditions over multiple drought environments during 2021–2024. A ‘hotspot QTL’ cluster consisting of six QTLs was detected for drought tolerance related traits viz. seed yield/plant, fresh weight of roots and shoots and chlorophyll content on linkage group 7. These QTLs detected under four environments were found to be strongly linked with drought tolerance and explained 48.83% phenotypic variance on a cumulative basis. Furthermore, the hotspot harboured several drought responsive functionally annotated genes.</p> Conclusion <p>The present study provides valuable insights into QTLs and SNPs associated with drought tolerance in lentil. The identification of a robust QTL hotspot region, together with key candidate genes, offers promising targets for fine mapping and development of marker assisted breeding strategies aimed at improving drought tolerance in lentil.</p>