The present investigation was carried out in the greenhouse from October 2009 to March 2010 included two main conditions, i.e. normal irrigation and water stress every 15 days using Line x tester analysis through the parents (Sakha 102 and Agami) were used as testers, while; the cultivars Giza 171, Giza 172, Gaori and Giza 159 were used as lines, and markers assisted selection techniques used a random primer namely; A17, A18 and As-467468 as indication for drought tolerance in rice. The main characters studied were yield and its components;(heading date, plant height, number of panicles/plant, number of filled grains/panicle, 1000-grain weight and grain yield/plant) and some characters related to drought namely;( maximum root length, number of roots/plant, root volume, root xylem, vessels number and root dry weight),respectively under normal and drought conditions. Heterosis over better parent, general and specific combining ability were studied as a genetic components. The most desirable mean value, positive and highly significant of heterosis, general and specific combining ability effects for all traits studied using line x tester design under the two conditions were shown in the genotypes; Agami, Gaori, Sakha 102 x Gaori, Agami x Gaori and Agami x Giza 159.  From the foreign discussion, it could be concluded that, the crosses; Agami x Gaori, Agami x Giza 159 and Sakha 102 x Gaori were contained of the bands number 1, 2 and 6 for A17 primer 3, 6 and 7 bands for A18 primer and the bands number 3, 4, 5, 7, 8 and 9 for As-467468 primer under drought conditions which indicated that these bands were found to be index for drought tolerance in rice. So these crosses would be effective and important for grown as lines of drought tolerance in rice.