The experiment was carried out in strip plot design with three replications to evaluate 14rice genotypes under normal and water deficit in the field and biotechnology lab of Rice research and Training Center at Sakha Agricultural Research Station, Sakha, Kafr EL-Sheikh Egypt, during2021 and 2022summer seasons. Results revealed a wide variation among rice genotypes and their parents for agronomical characteristics and SSR markers. Data showed that days to maturity, plant height, Flag leaf area, number of panicle-1 , Panicle length, number of filled and unfilled grains panicles-1 as well as grain yield t ha-1 were significantly affected by irrigation treatments. Grain yield was affected significantly according to the genotypes and irrigation treatments. The combination between Egyptian Yasmin with normal irrigation produced the highest values of grain yield with the lowest percentage(14.58%) of yield reduction compared to its production under water deficit conditions. While, the lowest values of grain yield were obtained with Nerica7 (V2) under water shortage conditions with the highest percentage(33.63%) of yield reduction compared to its production under normal irrigation. Fifty SSR markers were used for estimating the genetic variation among the 14rice genotypes. Rice genotypes were divided into two main groups based on the polymorphism revealed by the SSR markers. The first group has the aromatic genotype, Egyptian yasmine and the promising newly developed genotype No.2. While, the second main group has the other tested rice genotypes, NERICA7 and the other genotypes. The data indicated that phenotypic variance was generally superior than genotypic variance for all studied traits.