Magnesium (Mg(2+)) is abundant in plant cells and plays a critical role in many physiological processes. A 10-member gene family AtMGT (also known as AtMRS2) was identified in Arabidopsis, which belongs to a eukaryote subset of the CorA superfamily, functioning as Mg(2+) transporters. Some family members (AtMGT1 and AtMGT10) function as high-affinity Mg(2+) transporter and could complement bacterial mutant or yeast mutant lacking Mg(2+) transport capability. Here we report an AtMGT family member, AtMGT9, that functions as a low-affinity Mg(2+) transporter, and is essential for pollen development. The functional complementation assay in Salmonella mutant strain MM281 showed that AtMGT9 is capable of mediating Mg(2+) uptake in the sub-millimolar range of Mg(2+). The AtMGT9 gene was expressed most strongly in mature anthers and was also detectable in vascular tissues of the leaves, and in young roots. Disruption of AtMGT9 gene expression resulted in abortion of half of the mature pollen grains in heterozygous mutant +/mgt9, and no homozygous mutant plant was obtained in the progeny of selfed +/mgt9 plants. Transgenic plants expressing AtMGT9 in these heterozygous plants can recover the pollen phenotype to the wild type. In addition, AtMGT9 RNAi transgenic plants also showed similar abortive pollen phenotype to mutant +/mgt9. Together, our results demonstrate that AtMGT9 functions as a low-affinity Mg(2+) transporter that plays a crucial role in male gametophyte development and male fertility.