A 2x2 diallel mating design was set up to estimate quantitative genetic parameters after leaf artificial inoculation tests in nursery and field for three consecutive years. F12 and F40 families of two reciprocal crosses viz., F12: ♀SCA12 × ♂ICS40 and F40: ♀ICS40 × ♂SCA12 were used to study heterosis (midparent), heterobeltiosis (better-parent), heritability (narrow-sense and broad-sense) and to quantify total polyphenols (TPP) and total flavonoids (TF) contents after inoculation of the leaves of parental and hybrid cocoa genotypes with Phytophthora megakarya. The results of heterosis and heterobeltiosis exhibited hybrid vigor of 86.66 and 85%, respectively. The highest heritability was identified [narrowsense heritability (h²: 0.668 for F12 and 0.682 for F40) and broad-sense heritability (H²: 0.765 for F12 and 0.672 for F40)] for necrosis length in 2014. With regards to low narrow-sense heritability, it ranged from 0.019 to 0.162 while corresponding broad-sense heritability ranged from 0.476 to 0.562 for biochemical compounds. Among parent clones, ICS40 and SCA12 proved to have the general combining abilities (GCA). The use of these parental lines and understanding the gene flow of tolerance to black pod disease (Bpd) in cocoa will help researchers to develop a targeted breeding approach in generating new generation of tolerant genotypes cocoa.