Diseases are a major production constraint wherever cocoa (Theobroma cacao) is grown. The principal method of ameliorating cocoa production is the use of hybrid clones, which have resistance to important diseases and high productivity. To select new genotypes with resistance to Phytophtora megakarya, the cause of the destructive black pod disease, comparative analyses (quantitative and qualitative) of phenolics were conducted on the leaves of parental genotypes considered tolerant (SNK413) or sensitive (SNK10) to black pod disease and hybrids (families F16 and F3) derived from reciprocal crossbreeding between these two parental clones. A negative correlation between the size of necrotic lesions and the total phenolic content was demonstrated. Three individuals of the F16 family (F1612, F1614 and F1627), progenies from the ♀ SNK413 × ♂ SNK10 cross, had small lesions and high concentrations of phenolics. The F1612, F1614 and F1627 genotypes, which had performances similar to those of the tolerant parent SNK413 can be considered to be elite clones. The heterosis linked to containment of lesions revealed the manifestation of strong hybrid vigour for the genotype F1612 followed by F1614 and F1627. However, after analysis of total phenolics, no maternal effect was detected in the transmission of this character. Qualitative analyses of phenolic compounds by high performance liquid chromatography from the parents and individuals from the two families showed the accumulation of luteolin derivatives after inoculation in the SNK413 clone and individuals where the female parent was the SNK413 clone. This may indicate that some resistance characters of cocoa to Phytophthora spp. are cytoplasmic. These compounds among many other unidentified compounds have an essential role in the reaction and mechanism of defence of cocoa against P. megakarya.