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An excess of selenium (Se) can cause toxicity to plants. Treatment with melatonin (MT) can alleviate the stress conditions in plants. Limited research exists on the impact of MT on Se stress and uptake in fruit trees. To address Se stress and enhance Se accumulation in <i>Cyphomandra betacea</i> Sendt. (<i>Solanum betaceum</i> Cav.), the effects of exogenous MT (50–200 µmol L⁻¹) on <i>C. betacea</i> growth and Se accumulation under Se stress were studied. MT increased the biomass, photosynthetic pigments levels, and peroxidase activity of <i>C. betacea</i> under Se stress. Only at concentrations of 150 and 200 µmol L⁻¹ did MT increase superoxide dismutase and catalase activities, as well as soluble protein content in <i>C. betacea</i> leaves. MT treatment also boosted the Se content and bioconcentration factor of <i>C. betacea</i> under Se stress while reducing the translocation factor. The dose of MT was directly related to the Se content, and the highest levels of Se in roots and shoots were observed at 150 µmol L⁻¹, which was an increase of 114% and 60%, respectively, compared with the control. In addition, correlation, principal component, cluster, grey, and path analyses revealed a strong correlation between root Se content and shoot biomass with the shoot Se content. Therefore, MT treatment can mitigate Se stress and enhance Se uptake in <i>C. betacea</i>, and the most effective dose of MT is 150 µmol L⁻¹.