Abstract: Black pod disease caused by Phytophthora palmivora and Phytophthora megakarya is a serious constraint to cocoa (Theobroma cacao L.) yields in Ghana. To investigate the association between disease resistance and pod husk anatomical/histological traits, 8 cocoa genotypes were evaluated by leaf discs and detached pod inoculations and examination of anatomical factors. Width of vascular bundles, length of vascular bundles, epicarp thickness, distance between vascular bundles and epicarp, number of cells in epicarp and number of cells in mesocarp were negatively correlated with resistance to black pod disease. Number of vascular bundles and cell width were positively correlated with black pod disease resistance. Lower epicarp thickness and higher number of vascular bundles were observed in susceptible genotypes suggesting their porosity to Phytophthora species. The cells in epicarp and mesocarp were arranged more compactly in resistant than susceptible genotypes. Presence of extra thickness of phloem fiber and its gritty nature in resistance genotypes may act as strong mechanical barrier for penetration and absorption of sap from phloem. The cell walls of resistant genotypes stained deep red with phloroglucinol, a lignin specific stain, suggesting the presence of lignin. Principal components analysis showed that the first 2 components contribute to explain 98% of the total variation of anatomical traits. Number of cells in epicarp and number of vascular bundles were the major contributors to PC1 and PC2. The principal components, correlation coefficients, multiple and step-wise regressions indicated that number of vascular bundles, epicarp thickness, number of cells in epicarp and cell width were reliable histological traits and they could be used to screen and select for resistance to black pod disease of cocoa.