A set of hundred maize inbred lines were analyzed for resilience to moisture stress for twenty-four traits related to maturity, morphological, physiological, yield, quality and root traits. Evaluation confirmed a wide range of variability revealing significant response of main effects (lines, irrigations and years and their respective digenic and trigenic interactions). Fifteen elite identified lines performed well under moisture stress conditions showing inbuilt tolerance towards moisture stress. A set of 32 SSR markers, having genome-wide coverage, was chosen for genotyping the selected 15 inbred lines. These markers generated a total of 239 polymorphic alleles with an average of 7.47 alleles per locus. The minimum and maximum PIC value was 0.886 and 0.608 with a mean of 0.782. The coefficient of genetic dissimilarity ranged from 0.215 to 0.148. DARwin derived cluster analysis grouped 15 elite maize lines in three major clusters with five lines each in cluster-III and II and four lines in cluster-I with KDM-361A as root (at origin point. Molecular marker data however, confirmed diverse genetic nature of six lines (KDM-372, KDM-343A, KDM-331, KDM-961, KDM-1051 and KDM-1156) with favorable drought resilient traits with no yield penalty under moisture stress. Exploitation of these identified elite lines in involving all possible combinations helped to develop single cross hybrids under moisture stress conditions.