Abstract: This study was carried out, in order to investigate the genetic structure of the 36 maize hybrids established from eighteen female lines and two male testers according to linextester method under non water stress and water stress conditions. So, 36 generated hybrids were planted in two experiments with normal irrigation and water stress at grain filling stage in Iran in 2008, using a RBCD design with three replications. The results showed that the effect of gene action could be both non additive and additive in the expression of grain yield under both conditions. However, GCA/SCA variance ratio revealed that non additive genetic variance was more important for grain yield than additive variance. Grain yield recorded high genetic variance value under non water stress condition compared to those under water stress condition. Also, narrow and broad sense heritability estimates in non water stress condition were higher than water stress condition. The lines L8, L11 and L17 in non stress condition and the lines L15, L16 and L17 in stress condition showed better general combining abilities for grain yield. The crosses such as L1xT1, L4xT1 and L8xT1 in non stress condition and L9xT2 in stress condition showed better specific combining abilities for grain yield. For choosing high efficient drought tolerance indices (SSI, TOL, MP and STI), broad sense heritability, narrow sense heritability and correlation of these indices were estimated. The results showed that STI was a successful index to select high yield and tolerant genotypes in comparison to SSI and TOL indices. Based on yield in both conditions and STI, the crosses L1xT1, L4xT1, L8xT1 and L17xT1 had the best tolerance to water stress at grain filling stage.