Waterlogging is a major constraint to crop yield worldwide. In the soft winter wheat growing region of the eastern United States, yield losses as high as 30% have been observed in years with high rainfall during early vegetative growth. It is also predicted that global climate change will result in increased winter precipitation and waterlogging of cereals. Waterlogging causes an ‘energy crises’ due to the depletion of oxygen available to the plant for respiration, resulting in low ATP production. Wheat has developed different mechanisms to adapt to waterlogging including both anatomical and biochemical changes. Anatomical changes include the development of adventitious roots, aerenchyma and stem elongation. Differences in physiological traits such as photosynthesis, chlorophyll content and stomatal conductance have also been associated with variation for waterlogging tolerance. However, despite its impact on wheat yields, little is known about the genetic control of waterlogging tolerance. In this study we report data from a set of 130 Jaypee/USG3209 RILs segregating in their agronomic and physiological response to waterlogging. Jaypee is a waterlogging tolerant cultivar which maintains 15-20% higher vegetative and root biomass under waterlogging compared to USG3209. A strong phenotypic correlation and co-localization of QTL for flooding tolerance index (FTI), quantum yield of PSII and chlorophyll content was observed in the RIL population. Other genome regions show co-localization of QTL for FTI and root characteristics including root biomass and the formation of root aerenchyma. Current work is focusing on developing spectral reflectance indices for waterlogging tolerance and identifying associated QTL regions.