Striga asiatica is a major constraint to rain-fed rice (Oryza sativa L.) and maize (Zea mays L.) production in the Middle West and South regions of Madagascar. This work aims to establish a robust and efficient field and glasshouse screening protocol for identification of rice and maize mutants having resistance/tolerance to Striga asiatica by assessing the host plant phenotypic response under severe S. asiatica infestation in soil. Our screening strategy involved field and glasshouse experiments where soils were artificially infested with S. asiatica seeds under fertilizer-free growing conditions. Two maize (Plata and IRAT200), and two rice (B22 and F154), farmer-preferred Striga susceptible varieties, gamma irradiated at different doses were screened in a Striga endemic area of the Middle West and compared to their respective unmutagenized lines. Rice M3 to M5 progenies were also screened in Striga infested pots in a glasshouse. Developed protocols enabled the production of promising new Striga resistant/tolerant varieties in both maize and rice adapted to Malagasy agriculture.