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Magnesium (Mg2+) is one of the essential cations in all calls. Although the Mg2+ transport mechanism has been well-documented in bacteria, less is known about Mg2+ transporters in eukaryotes. The AtMGT gene family encoding putative magnesium transport proteins had been described previously. We report here that one of the Arabidopsis MGT family members, the AtMGT7 gene, encodes two mRNAs that have resulted from alternative splicing variants, designated AtMGT7a and AtMGTTb. Interestingly, the two mRNA variants were expressed with different patterns with AtMGT7a expressing in all organs, but AtMGTTb appearing only in root and flowers. The AtMGT7a variant functionally complemented a bacterial mutant lacking Mg2+ transport capacity, whereas AtMGT7b did not. The 63Ni2+ tracer uptake analysis in the bacterial model showed that AtMGT7a mediated low-affinity transport of Mg2+. Consistent with the complementation assay result, 63Ni2+ tracer uptake analysis revealed that AtMGT7b did not transport Mg2+. This study therefore has identified from a higher plant the first low-affinity Mg2+ transporter encoded by a gana with alternatively spliced transcripts that produce proteins with distinct functions.