Melatonin, the chief secretory product of the vertebrate pineal gland is also known to occur in numerous photoautotrophic organisms. The indoleamine is suspected to act as a transducer of photoperiodic information and/or to participate in antioxidative protection. In higher plants and other photoautotrophic organisms, contradictory results for melatonin content for samples from the same species show that further improvement of methods for reliable quantification is required. In the present study, melatonin was quantified in tomatoes, ginger and the marine green macroalga, Ulva lactuca, after extraction with three different extraction methods based on ether, acetone or perchloric acid. Melatonin was determined by enzyme-linked immunosorbent assay (ELISA) in high-performance liquid chromatography (HPLC)-purified extracts. The same HPLC system used for purification of extracts was used for parallel quantifications after derivatization of melatonin under alkaline conditions in the presence of hydrogen peroxide (HPLC-PD). Both quantification methods gave similar results with a high correlation [f(x) = 0.99x + 3.01; R(2) = 0.99]. In ginger, the melatonin concentration was below 5 pg/g (fresh weight, f.w.), whereas in tomatoes about 1200 pg/g (f.w.) were found, and in the green alga, U. lactuca, approximately 12 pg/g (f.w.). Taking into account the recovery rates for synthetic melatonin added prior to extraction, no substantial differences were observed in melatonin quantification between different extraction methods. The demonstrated methods based on HPLC purification and subsequent quantification by ELISA and HPLC-PD allow highly sensitive melatonin determinations in diverse photoautotrophic organisms with a low risk of overestimations by false-positive results.