Rice cultivation in the islands encounters submergence at various growth stages leading to Substantial yield and quality loss. Continuous and heavy rainfall during a short-span leads to water logging and continuous submergence even up to five days. Developing submergence/flooding tolerant versions of adapted elite rice genotypes helps to reduce the yield loss in these areas. The present study was undertaken to evaluate the physiological response of rice genotypes adapted to island conditions under submergence stress. The outcome of the study will help to identify promising donor for breeding submergence stress tolerance cultivars with the background of popular rice varieties of A&N islands. The tolerant genotypes like Black Burma, IR64 Sub1, revealed that they posses many of the adaptive traits like slower elongation during submergence, chlorophyll retention, higher stem reserves post submergence, higher survival per centage required for the flood-prone island ecosystem.