The direct determination of elemental concentrations in plants is laborious. To overcome this, a novel monitoring system for magnesium (Mg) in plants was established. Mg deficiency-induced genes were identified by microarray analysis and transgenic lines that expressed luciferase (LUC) under the control of the Mg deficiency-inducible CAX3 promoter were established. The transgenic lines showed a clear response under low Mg conditions, and the degree of luminescence reflected the accumulation of endogenous CAX3 mRNA. The CAX3 expression pattern was also examined in a previously characterized low Mg-sensitive mutant, mrs2-7. In mrs2-7 mutant plants, CAX3 expression was more than three times higher than in the wild-type. In addition, CAX3 expression was negatively correlated with the shoot Mg concentration. Together, these results indicate that CAX3 transcription is a quantitative marker of the Mg status in Arabidopsis.