Anthocyanins are important components in the peel of red pears and contribute to the appearance of the fruit.  Melatonin application is known to affect anthocyanin biosynthesis, but the effect of preharvest melatonin application on fruit coloration remains largely unknown.  The objective of this study was to determine the effects of preharvest melatonin application on pigmentation, phenolic compounds, and the expression of related genes in Nanhong pear (Pyrus ussuriensis).  The applications were performed during the pre-color-change period by spraying 50 or 200 μmol L^–1 of melatonin on fruits.  We found that treatment with melatonin had a significant effect on color development.  The concentrations of anthocyanins and favonols were enhanced by melatonin treatment, whereas hydroxycinnamate and favanol concentrations were reduced.  Quantitative real-time PCR analyses indicated that the transcription levels for most anthocyanin biosynthetic genes and anthocyanin-related transcription factors were induced by melatonin.  Melatonin application also stimulated the expression of melatonin biosynthesis-related genes and consequently caused an increase in endogenous melatonin concentration.  These results provide insights into melatonin-induced fruit coloration and will facilitate the application of exogenous melatonin in agriculture.