Cut anthurium flowers can develop chilling injury, which is manifested as spathe browning during low temperature storage. Exogenous melatonin at 1, 10, 100 and 1000 μM ameliorated chilling injury in cut anthurium flowers by 11, 29, 51 and 31%, respectively, compared with that of untreated flowers, during storage at 4 °C for 21 d. Ameliorating chilling injury in flowers treated with 100 μM melatonin was accompanied by lower electrolyte leakage and malondialdehyde concentration during cold storage. Higher NADPH oxidase activity may be responsible for signaling H2O2 concentration in flowers treated with 100 μM melatonin than untreated flowers during storage at 4 °C for 7 d. Higher proline concentration in flowers treated with melatonin than untreated ones may result from higher proline 5-carboxylate synthetase and ornithine aminotransferase activities, and lower proline dehydrogenase activity during cold storage. Higher phenolic concentrations in treated flowers than in untreated ones may be attributed to higher phenylalanine ammonialyase activity and lower polyphenol oxidase activity that would result in greater DPPH scavenging capacity. Higher alternative oxidase gene expression accompanied by higher activities of catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase, and higher ascorbate and glutathione concentrations may be responsible for ameliorating damaging H2O2 concentration in melatonin treated flowers than in untreated flowers during storage at 4 °C for d. Exogenous melatonin can ameliorate chilling injury in cut anthurium flowers during low temperature storage.