Improvement of cooking and eating quality traits is one of the main target of several rice breeding program. The utilization of molecular markers to study genetic variation in specific regions for genome of rice is a useful index which may be used in rice breeding programs to use marker assisted selection (MAS). Eight microsatellite markers (SSR) closely related to major QTLs controlling three main proprieties for grain quality of rice (amylose content, gelatinization temperature and gel consistency) were used to group 40 rice genotypes in this study. The 40 genotypes tested were divided into six clusters based on their genetic distance. Cluster IV has the most genotypes (16), followed by cluster III with eight genotypes, and cluster V with only two genotypes. Cluster V and VI had the maximum inter-cluster distance (35.627), whereas cluster III and VI had the lowest (5.897). There were a total of 39 polymorphic alleles, with an average of 4.875 alleles per SSR locus. The number of alleles per locus ranged from 3 in RM276 to 6 in both of RM204 and RM340. Effective number of alleles ranged from 2.253 to 5.019 alleles at RM276 and RM204, respectively, with an average of 3.894 alleles per locus. The average heterozygosity was 0.752, showing substantial genetic variation among the genotypes investigated, according to Nei's gene diversity. The 40 genotypes investigated were sorted into six groups by cluster analysis using the UPGMA method, which differentiated the Egyptian genotypes with good cooking and eating quality from the others. The Egyptian japonica genotypes were classified with good cooking and eating properties with low amylose content, low gelatinization temperature and soft gel consistency. SSR markers related to genes or QTLs controlling grain cooking and eating qualities were found to be an effective technique for marker assisted selection (MAS) to assess rice grain quality in this study.