Plant stomata play an important role in CO2 uptake for photosynthesis and transpiration, but the mechanisms underlying stomatal opening and closing are still not completely understood. Here, through large-scale screening, we identified an Arabidopsis mutant (cst2 for closed stomata2) defective in stomatal opening under light condition. A map-based cloning combined with complementation test revealed that the mutant phenotype was caused by a nucleotide substitution of a gene, which domains show similarity to human Mg efflux transporter ACDP/CNNM. Functional analysis showed that CST2 encodes a tonoplast-localized transporter for Mg. This protein is constitutively and highly expressed in the guard cells. Furthermore, CST2 is phosphorylated by calcineurin B-like protein (CBL)-interacting protein kinases 26 (CIPK26) in vitro, which is probably required for its activation. Knockout of this gene resulted in stomatal closing and growth retardation under high Mg concentration conditions, while over-expression of this gene increased tolerance to high Mg. Our results indicate that CST2 plays an important role in maintaining Mg homeostasis in plant cells through sequestering Mg into vacuoles especially in guard cells and that this homeostasis is required for stomatal opening, which provide a novel insight into mechanism of stomatal opening in plants.