A new species of Myrtaceae, Syzygium halmaherense, is described from the Weda Bay area of Halmahera, Maluku, Indonesia. Syzygium halmaherense resembles S. perspicuinervium but differs in leaf and flower morphology. Syzygium halmaherense has shorter petioles, cordate bases, acute to obtuse apices, and lacks abaxial glandular-puncticulate, unlike S. perspicuinervium with longer petioles, broadly acute bases, acuminate apices, and numerous glandular-puncticulate. Syzygium halmaherense has panicle inflorescences with larger flowers, free sepals, and subcalyptrate petals, while S. perspicuinervium has fascicled or solitary inflorescences, smaller flowers, calyptrate sepals, and ovate petals. Scanning electron microscope analysis of S. halmaherense shows paracytic stomata on the abaxial leaves and monad pollen with a concave triangular shape, 3-syncolporate structure, sub-oblate P/E ratio, and weakly ornamented exine.