A new species of Theobroma from the Southern Pacific coast of Costa Rica is described and illustrated. Theobroma flaviflorum is restricted to the Osa Peninsula, where it has been collected on stream banks. The new species shows an unusual combination of characters including yellow flowers and globose mature fruits without ribs that are slightly sunken toward the apex and borne on terminal leafy terminal branches. The new species is compared with T. angustifolium, T. cirmolinae, and T. stipulatum which also have flowers that are yellow or orange; and with T. grandiflorum, T. hylaeum, and T. subincanum, which have similarly shaped fruits. A key for the Mesoamerican species of Theobroma is provided, as well as some notes for two of the species of Theobroma also reported for this region.