Manganese phytotoxicity is an important edaphic stress that is poorly understood. Fernando and Lynch review processes regulating Mn availability in soils, mechanisms of Mn phytotoxicity and possible mechanisms for accounting for the large variation in Mn tolerance among plant taxa. The strong effects of light, temperature, precipitation and other climate variables on Mn phytoavailability and phytotoxicity suggest that global climate change is likely to exacerbate Mn toxicity in the future, which has largely escaped scientific attention. Large inter- and intra-specific genetic variation in tolerance to Mn toxicity suggests that increased Mn toxicity in natural ecosystems may drive changes in community composition, but that in agroecosystems crops may be developed with greater Mn tolerance.