Eleven hybrid rice combinations were produced by using three cytoplasmic male sterility lines and seven restorers (line x tester mating design) evaluated for agronomic and yield characters under normal and salt soil conditions.The genotypes, Pusa 6A; Giza 178; GZ5121; IR69625A; IR69625A x PR1; Pusa 6A x Giza 178; IR69625A x GZ5121  and IR69625A x PR3 gave the lowest reduction for yield under saline soil condition. However, the genotypes IR69625A x GZ5121 (3.34 t./fed.) and IR69625A x PR3 (3.27 t./fed.) gave the highest yield under saline soil condition if compared with Giza 178 (2.94 t./fed.).Simple sequence repeat (SSR) markers were used to detect possible specific marker to be utilized in the hybrid rice future breeding programs for salt tolerance. However, SSR markers; RM21, RM302 and RM315 generated two (140, 170 bp), three (120, 170, 350 bp) and five DNA fragments (110, 130, 170, 180, 190 bp), respectively. These band can be used as positive or negative specific DNA band on the basis of their appearance or disappearance in the different gene types under study. It is of great interest to mention that the three DNA bands, 140 bp (RM21), 120 bp (RM302) and 190 bp (RM315) are considered as positive specific marker for salt tolerance, while they were appeared in the tolerant genotype (Giza 178) and other hybrid rice genotypes. These salt tolerant specific bands were found in the next genotypes; Pasua 6A x Giza 178, IR68902A, IR68902A x PR1, IR68902A x PR2, IR68902A x PR3, GZ6296R and Giza 182 may be due to heterosis effect, the origin or salt tolerant.Based on phylogenetic tree using similarity index, Pusa 6A x Giza 178, Pusa 6A x PRI, Pusa 6A x PR3 genotypes were found in one cluster and were closely related to the tolerant genotype Giza 178. On the other hand, phylogenetic tree showed that other four clusters were separated and proved that the genotypes PR2; PR3; GZ5121R; IR69625A x PR2; IR69625A x PR3 and IR69625A x GZ5121R were closely related to each other on the basis of their ability to tolerate salt stress.