The efficiency of microsatellite (SSR), random and semi-random (RAPD and ISJ) molecular markers for fingerprinting of rice hybrid cultivars was investiged. Three cytoplasmic male sterility (CMS) lines, five restorer lines and their eight hybrids combination were used in this study. From 14 SSR markers used, 10 markers had polymorphism among genotypes. The average number of band per primers and per genotypes were 1.92 and 1.68, respectively. The SSR markers amplified unique fingerprint for the restorer lines while two CMS lines (Neda-A and Nemat-A) and in turn their resultant hybrids could not be differentiated. IRH1 the first Iranian aromatic hybrid rice differentiated from other hybrids and produce unique fingerprint. Non-parental extra band were observed when the F 1 's SSR product analyzed electrophorectically. They might be heteroduplex DNA fragments formed by identical fragments amplified from allelic sequence. Genetic purity of F 1 hybrids was examinated using SSR markers and heteroduplex bands. Cluster analysis based on shared allelic similarity coefficient using UPGMA, grouped the rice genotypes into three clusters, each of which containing 43.75%, 43.75%, and 12.5% of genotypes. The results of RAPD fingerprinting with 15 primers reveal that out of 155 produced band, 102 (65.8%) was polymorphic. The average number of band per primer and per genotypes was 10.3 and 9.7, respectively. Polymorphic RAPD markers used for identification and fingerprinting rice cultivars and hybrids and the result indicated that RAPD analysis can be used for characterization rice genotypes. The genetic similarity among cultivars and lines ranged from 0.25 to 0.91 with an average similarity index of 0.58. Based on this markers all hybrids were similar to seed parent. Cluster analysis based on Jaccard's similarity coefficient using UPGMA procedure grouped the cultivars and lines into five clusters, each of which containing 62.5%, 12.5%, 12.5%, 6.25 and 6.25% of genotypes. The results of ISJ fingerprinting using 12 selected primers showed that out of 185 produced bands, 79 (42.7%) were polymorphic. The average number of band per primer and per genotypes were 11.1 and 5.6, respectively. Polymorphic ISJ markers used for identification and fingerprinting rice cultivars and hybrids, and hence showing that semi-random analysis can be used for characterization rice genotypes. The genetic similarity among cultivars and lines ranged from 0.47 to 0.95 with an average similarity index of 0.75. Number of polymorphic DNA fragments in IR58025A/IR42686R، Nemat-A/IR62037-93-1-3-1-IR, Nemat-A/IR69726-54-3-IR and Nemat-A/IR28 hybrids had greater similarity to those of female than male, while Nede-A/IR69726-54-3-IR، Nede-A/IR28, Nede-A