Maize genotypes including 64 in number were evaluated at early stage in greenhouse with the soil having 40-100% moisture levels for different seedling parameters on various genetic analysis revealed that the highest estimates of heritability were found for root fresh weight, root volume and shoot fresh weight, at 40% soil moisture providing the evidence that these plant characters are under the control of additive genetic effects. The results showed that selection should evolve the genetic material with improved characteristics within short time. The single linkage cluster analysis and principle component analysis identified the variation among these parameters and in genotypes under the different moisture levels. Genotypes 21 in number with moderately tolerant and drought susceptible backgrounds were further evaluated by using Inter simple sequence repeats markers to ascertain their biodiversity. So 14 number of parents with determined diversity were finally selected and were crossed in line x tester fashion and their F1 along with their related parents were grown using randomized complete block design with 3 replications under normal and 50% of normal irrigation field conditions. All the cultural and other practices were kept uniform to both plantings except irrigation. Various agronomic and physiological parameters were recorded and analyzed for analysis of variance, genotypic and phenotypic correlation, principle component analysis, cluster analysis, general combining ability analysis and specific combining ability analysis for both conditions. Highest range of broad sense heritability with higher genetic advance regarding different plant characteristics depicted that these plant characters were controlled by additive genetic effects. So, it indicates that a fast genetic improvement is found in the experimental material. Clusters with superior genotypes showed the genetic potential of accession to transfer the desirable genes to improve yield in maize. The best combiners for both normal and 50% of normal irrigation field conditions were L3 x T4 (015114 x EV-6098), L9 x T4 (015129 x EV-6098), L9 x T1 (015129 x Sahiwal-2002). These crosses might be useful as transgressive seggregants in subsequent generations. The lines viz 014955, 015084, 015114, Sahiwal-2002, Agaiti-2002, Ev-5098 and Ev-6098 were found as best parents. These lines may be exploited in future breeding program for drought conditions. On the basis of different inheritance pattern of each parameter, it was suggested that overall performance of the lines and their all possible combinations might be more useful while selecting for water stress condition.