The aim of this study was to assess the chemical composition and the antimicrobial activity of essential oils of dried fruits and buds of Zanthoxylum xanthoxyloides (Z. xanthoxyloides) and Syzygium aromaticum (S. aromaticum or clove), respectively, against Phytophthora megakarya (P. megakarya). Essential oils were extracted by hydrodistillation, and their composition was determined by gas chromatography and by gas chromatography coupled with Mass Spectrometry. The minimal inhibitory concentration (MIC) and minimal lethal concentration (MLC) of the essential oils against P. megakarya were assessed by the Agar dilution method. The in vivo efficacy study consisted of spraying the essential oil emulsions on cocoa pod husk pieces (CPHP), followed by the inoculation with P. megakarya zoospores. The hydrodistillation yielded 10.54 and 1.89% of essential oils for S. aromaticum and Z. xanthoxyloides, respectively. Both oils were mainly made up of oxygenated monoterpenes (89.58 and 88.2%, respectively). Eugenol (83.02%) and eugenyl acetate (9.15%) were the main components of clove oil while α-citronelol (25.83%) and trans-geraniol (16.49%) were mostly found in the Z. xanthoxyloides oil. Clove oil exhibited stronger antimicrobial activity with a MIC of 250 μl/l than Z. xanthoxyloides with MIC of 350 μl/l. The symptoms were totally suppressed on pod husk treated with clove oil at 2000 μl/l. The decrease in the growth rate of the necrosis (GRN) and the sporulation of P. megakarya (PS) on cocoa husk after the successful infection was significant after the treatment with essential oils. These results are promising and indicate that the studied essential oils might be further investigated as natural alternatives to synthetic fungicides for the control of cocoa black pod diseases.