Sources of tolerance and a reliable trait evaluation method are crucial in breeding for abiotic stress tolerance. Waterlogging is one of the most important abiotic stresses in high rainfall areas. Waterlogging tolerances have been reported in different plant species. However, the complexity of the trait makes it very difficult to evaluate, thus hard to breed for. A reliable screening method can make the breeding programme more successful. This chapter will summarize: genetic resources and genetic behaviour of waterlogging tolerance; different selection criteria; and QTLs controlling the tolerance. The importance of accurate phenotyping in screening for QTLs controlling the tolerance is also discussed.