In this paper, we develop an epidemiological model with both environmental (primary infection from the environmental spores reservoir) and direct transmission (secondary infection from an infected host to a susceptible pod). This model simulates the spatiotemporal evolution of cocoa black pod disease caused by Phytophthora megakarya. Since reliable parameter estimation is a central issue for modeling realistic biological systems, we used a mechanistic–statistical approach to estimate model parameters from real observations of a specific cocoa plot. In addition, to refine numerical simulations of the pathosystem, data describing the shade intensity all over the plot were exploited and led to increased model predictions accuracy and also highlighted a higher number of infected pods located in areas of the plot with higher shading intensity. Recommendations in terms of promoting cocoa farming in systems with low shading intensity may be evident if these results are confirmed. Our results also highlight the importance of the environmental spore reservoir in black pod disease dynamics.