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Climate change and the consequent increase in the incidence of drought and flood will remain a major threat to smallholders. Hence, it is crucial to adopt an appropriate adaptation strategy to overcome this threat and increase farmers’ income. Because seed is a primary input, the adoption of stress-tolerant rice varieties is a potential mitigation strategy to combat climate risks. In this context, the present study is carried out among paddy farmers in the flood-prone region of Eastern India to understand the adoption and impact of submergence-tolerant rice variety Swarna-Sub1 on yield and income. The study reveals that the adoption of Swarna-Sub1 varies significantly across eastern India. Education, primary occupation, credit, social group, cultivated land, and access to information on stress-tolerant rice varieties significantly influence the adoption decision. Endogenous switching regression estimates revealed that the expected paddy yield of Swarna-Sub1 adopters in an actual scenario and for non-adopters in a counterfactual scenario is significantly higher than for their counterparts. The average treatment effect confirms that the benefit of cultivating Swarna-Sub1 is much higher in submergence conditions than in normal conditions. An additional 19.0% and 48.2% of paddy yield and income is obtained respectively by cultivating Swarna-Sub1 in flooded conditions.