High temperature is a major environmental stress factor limiting rice productivity. The present investigation was carried out to evaluate and identify heat tolerant rice genotypes on the basis of heat indices and SSR markers. Fifteen rice genotypes were designed in Randomized Complete Block Design (RBCD) with three replications under well-watered and heat stress conditions at two environmentally different sites (Sakha and New Vally) during 2018 and 2019 rice season. Parameters of heat indices were calculated based on grain yield under both conditions. The results indicated that the heat tolerant index (HTI) and mean productivity (MP) index had the highest correlation with yield under two the conditions, Giza178, Giza179, Giza182, Egyptian Yasmin, Egyptian Hybrid1 and N22 were the best genotypes based on indices values, representing high temperature tolerance of these genotypes. Results of variance analysis of yield and other traits in both conditions showed that there was a significant difference among genotypes and their traits. Egyptian hybrid 1 produced the highest mean values of grain yield/plant under normal and heat stress conditions (50.26 and 37.00 g/plant), meanwhile Sakha102 had the highest reduction (70.36%) and N22 had the lowest reduction (23.9%).All genotypes clearly grouped into two major clusters in the dendrogram at 58% similarity based on Jaccard's similarity index. The first cluster represents the Indica and Indica/Japonica tolerant rice genotypes for high heat, while the second cluster represents the Japonica sensitive genotypes for high heat.