© 2014 German Botanical Society and The Royal Botanical Society of the Netherlands. Vast agricultural areas are affected by flooding, causing up to 80% yield reduction and resulting in multibillion dollar losses. Up to now, the focus of plant breeders was predominantly on detrimental effects of anoxia, while other (potentially equally important) traits were essentially neglected; one of these is soil elemental toxicity. Excess water triggers a progressive decrease in soil redox potential, thus increasing the concentration of Mn2+ that can be toxic to plants if above a specific threshold. This work aimed to quantify the relative contribution of Mn2+ toxicity to waterlogging stress tolerance, using barley as a case study. Twenty barley (Hordeum vulgare) genotypes contrasting in waterlogging stress tolerance were studied for their ability to cope with toxic (1 mm) amounts of Mn2+ in the root rhizosphere. Under Mn2+ toxicity, chlorophyll content of most waterlogging-tolerant genotypes (TX9425, Yerong, CPI-71284-48 and CM72) remained above 60% of the control value, whereas sensitive genotypes (Franklin and Naso Nijo) had 35% less chlorophyll than 35% of controls. Manganese concentration in leaves was not related to visual Mn2+ toxicity symptoms, suggesting that various Mn2+ tolerance mechanisms might operate in different tolerant genotypes, i.e. avoidance versus tissue tolerance. The overall significant (r = 0.60) correlation between tolerance to Mn2+ toxicity and waterlogging in barley suggests that plant breeding for tolerance to waterlogging traits may be advanced by targeting mechanisms conferring tolerance to Mn2+ toxicity, at least in this species.