A rapid screening method for Mn2+ tolerance in barley was developed using two varieties with different waterlogging tolerance. In this screening protocol plants were treated with 1 mM Mn2+ after germination in a hydroponic system for ten days. Chlorophyll contents and Mn concentrations were measured at the end of the treatment. Chlorophyll content in most waterlogging tolerant genotypes (TX9425, Yerong, CPI and CM72) remained at, or above, 65% of the control value. In contrast, waterlogging sensitive genotypes, Franklin and Naso Nijo, showed much greater reduction in chlorophyll content, with relative SPAD value being less than 15% of the control. Mn concentrations in leaves of sensitive varieties Franklin and Gairdner were also up to 2.3 times higher than in tolerant genotypes. This screening protocol will be used to identify the QTL for Mn2+ tolerance in a DH population of Yerong/Franklin, and the position of the QTL will be compared to that of the QTL for waterlogging tolerance identified in our previous studies.