Developing new tolerant varieties for water shortage condition is the best way to overcome water limitation problem. Using the selection of the best rice lines under stress condition could be useful strategy during breeding for tolerant genotypes. The present study aimed evaluate new promising lines along with their parental varieties Sakha 105 and IRAT 170 to identify superior lines under water shortage conditions. Field experiments were conducted at Rice Research and Training Center, Sakha, Kafr Elsheikh, Egypt during 2015 and 2016 rice growing seasons. This study was established in order to identify adapted and promising lines under both normal and water shortage conditions. The obtained results revealed that all promising lines showed good performance under both normal and stress conditions, the promising lines PL3, PL4 and PL6 showed the highest yield potential under normal conditions, with values 1246.7, 1071.7 and 990g/m² respectively, which were higher than the high-yielding parental variety Sakha 105. While the promising lines PL5, PL6 and PL10 showed the highest yield under water shortage conditions with values (738.3, 709 and 736.7 g/m²) higher than the tolerant parental variety IRAT 170. The promising lines PL2, PL5 and PL10 showed the lowest yield reduction caused by water stress according to drought susceptibility index (DSI) values (0.232, 0.255 and 0.181). These promising lines will be further evaluated for grain quality on multi-locations yield trials and could be used as a donor to improve cultivars ability for tolerance of water shortage condition. Significant amounts of genetic variations were observed for all studied traits. The phenotypic coefficient of variation (PCV) was greater than the genotypic coefficient of variation (GCV) in all studied traits. High broad sense heritability and genetic advance as percent of mean was observed for most studied traits indicating the importance of genetic variance for the studied traits. The SSR markers RM259, RM241, RM263 and RM201 showed a polymorphic pattern among the susceptible and tolerant genotypes with different alleles which detected at molecular weight ranged between 80bp to 190 bp. These markers could be used for the screening in further studies. The molecular analysis confirmed the existence of significant amounts of genetic variations, and hence the usefulness of studied materials for improving water deficit tolerance breeding program.