In order to characterize the self-incompatibility system in Theobroma cacao, the levels of ethylene, indole-3-acetic acid (IAA), and abscisic acid (ABA) were determined after pollination with compatible and incompatible pollen and in unpollinated flowers. Pollen tube growth rates after incompatible and compatible pollinations were identical, and the majority of the pollen tubes reached the ovules between 12 and 20 hours after pollination. ABA levels rose in incompatibly pollinated flowers, and fell in compatibly pollinated flowers, prior to pollen tube—ovule contact. Ethylene evolution remained stable in compatibly pollinated flowers and rose in incompatibly pollinated flowers. IAA concentrations increased in compatibly pollinated flowers, and remained stable in incompatibly pollinated flowers after pollination and subsequent to pollen tube—ovule contact.