Rice is highly susceptible to heat stress, particularly during the reproductive and ripening stages. Most of the prevalent high yielding red grained rice varieties in Kerala (South India), are highly susceptible to heat stress. Hence it is the need of the hour to impart heat tolerance to such varieties to reduce the yield loss thereby enhancing the production to a great extent. To address this, Uma (a highly popular red grained rice variety of Kerala) was crossed with Nagina22 (N22), the donor rice variety for heat tolerance. In MAS, a marker tightly linked to the desirable gene would help in selecting that specific gene with high precision and hence more reliable than selection based on only morphological traits. This paper discusses about the morphological and marker assisted selection with linked SSR markers for heat tolerance in the early segregating generations of this tropical rice hybrid.