Lowlands constitute one of the largest and most appropriate environments for rainfed rice cultivation in West Africa. In the context of climatic change, drought is among the most important abiotic constraints in this environment. The Generation Challenge Program (GCP) funds an innovative breeding program based on marker-assisted recurrent selection (MARS) for developing drought-tolerant cultivars with high yield under normal water regime, and good yield under drought stress. The detection of relevant association between molecular markers and phenotypes depends on improved methods for high-quality high-throughput phenotyping in the field. The project uses two phenotyping methods: (1) yield and yield components are evaluated under two hydric conditions (irrigated and stressed), and (2) during the drought period, the plant transpiration capacity is estimated through measurement of the canopy temperature. Plant canopy temperature acts as a good indicator of the plant water status as, when plants are undergoing water stress, their temperature increases. These changes in canopy temperature, relative to ambient temperature, result from the modification of plant transpiration through stomatal conductance control. A bi-parental indica population of 230 F3:5 lines derived from a cross between IR64 and B6144F, and 10 control varieties, were phenotyped under drought conditions at the International Center for Tropical Agriculture (CIAT) Villavicencio experimental station (Colombia) during the dry season 2012/13. Irrigation was suspended for 2 weeks at reproductive stage (45-60 days after sowing). Drought response was evaluated on the basis of canopy temperature obtained with a numerical infrared thermographic camera. The methodology was improved by introducing the crop water stress index (CWSI) calculated using climatic data collected from an on-site weather station to normalize canopy temperatures against micro-meteorological weather fluctuations. Leaf canopy temperature at rep