Magnesium (Mg ²⁺ ) homeostasis is critical for metabolism. However, the genetic determinants of the renal handling of Mg ²⁺ , which is crucial for Mg ²⁺ homeostasis, and the potential influence on metabolic traits in the general population are unknown. We obtained plasma and urine parameters from 9099 individuals from seven cohorts, and conducted a genome-wide meta-analysis of Mg ²⁺ homeostasis. We identified two loci associated with urinary magnesium (uMg), rs3824347 (P=4.4×10 ^-13 ) near TRPM6, which encodes an epithelial Mg ²⁺ channel, and rs35929 (P=2.1×10 ^-11 ), a variant of ARL15, which encodes a GTP-binding protein. Together, these loci account for 2.3% of the variation in 24-hour uMg excretion. In human kidney cells, ARL15 regulated TRPM6-mediated currents. In zebrafish, dietary Mg ²⁺ regulated the expression of the highly conserved ARL15 ortholog arl15b, and arl15b knockdown resulted in renal Mg ²⁺ wasting and metabolic disturbances. Finally, ARL15 rs35929 modified the association of uMg with fasting insulin and fat mass in a general population. In conclusion, this combined observational and experimental approach uncovered a gene-environment interaction linking Mg ²⁺ deficiency to insulin resistance and obesity.