To contribute to the taxonomic knowledge of barnacles in this understudied area, the first checklist of barnacles from the Moluccas is presented, including additional information on morphology, distribution, and substrate as well as molecular data. The species of barnacles from the Moluccas have been determined using morphological analysis and DNA sequences. During 19 field trips conducted between January 2016 and September 2017, 1,513 specimens of 24 species of intertidal and one species of deep-sea barnacles were collected from 51 localities from the islands. Morphological and molecular analysis of the collected material detected members of three families of stalked barnacles and four families of acorn barnacles. In addition to sampling in the field, we also surveyed the literature on barnacles from the Moluccas. In total, our checklist comprises 97 species from the Moluccas including 23 new records, two of them yet to be described species. Results suggest that the Moluccas have a much higher diversity of barnacles than previously known, for example, from the reports of Challenger and Siboga expeditions. For further work, routine application of molecular systematics could aid the detection of cryptic species, while increased sampling of more islands and a taxonomic revision of several groups would likely lead to an even higher number of species than currently known.