The hormone melatonin (N-acetyl-5-methoxytryptamine) is an indole derivative with a flexible peptide-like side chain attached at the C3 position. Using a combination of two-color resonant two-photon ionization (2C-R2PI), laser-induced fluorescence excitation (LIF), resonant ion-dip infrared spectroscopy (RIDIRS), fluorescence-dip infrared spectroscopy (FDIRS), and UV-UV hole-burning spectroscopy, the conformational preferences of melatonin in a molecular beam have been determined. Three major trans-amide conformers and two minor cis-amide conformers have been identified in the R2PI spectrum and characterized with RIDIRS and FDIRS. Structural assignments are made using the infrared spectra in concert with density functional theory and localized MP2 calculations. Observation of cis-amide melatonin conformers in the molecular beam, despite the large energy gap (approximately 3 kcal/mol) between trans- and cis-amides, is striking because there are at least nine lower-energy trans-amide minima that are not detected. The implications of this observation for cooling and trapping conformational population in a supersonic expansion are discussed.