Few studies have been carried out on the medical flora of Mexico's Yucatan Peninsula in search for new therapeutic agents, in particular against cancer. In this paper, we evaluated the cytotoxic potential of the extract of Bonellia albiflora, a plant utilized in the traditional Mayan medicine for treatment of chronic injuries of the mouth. We carried out the methanolic extracts of different parts of the plant by means of extraction with the Soxhlet equipment. We conducted liquid-liquid fractions on each extract with solvents of increasing polarity. All extracts and fractions were evaluated for cytotoxic activity versus four human cancer cell lines and one normal cell line through a tetrazolium dye reduction (MTT) assay in 96-well cell culture plates. The methanolic root-bark extract possessed much greater cytotoxic activity in the human oropharyngeal cancer cell line (KB); its hexanic fraction concentrated the active metabolites and induced apoptosis with the activation of caspases 3 and 8. The results demonstrate the cytotoxic potential of the B. albiflora hexanic fraction and substantiate the importance of the study of the traditional Mayan medicinal plants.