As drought is a major production constraint, there is a need to develop drought tolerant varieties which in turn requires identification of genotypes that carry genes or QTLs associated with drought tolerance. Hence, the objectives of this study were to identify and map chromosomal regions associated with drought tolerance and to identify SSR markers tightly linked to these QTLs and to identify drought tolerant sorghum genotypes. Phenotypic and genotypic coefficients of variations were moderately high at both locations. The population structure analysis revealed four distinct clusters for 151 accessions studied. A total of four SSR markers were found to be consistently associated with days to 50% flowering, panicle exsertion and grain weight per panicle. These markers were localized with previously identified markers. Hence, the identified markers could be used in future marker-assisted selection programmes