Abstract: Cocoa Swollen Shoot Virus (CSSV) occurs in all cocoa growing regions of Ghana and other parts of the West African sub-region. Cocoa swollen shoot virus disease has a long latent phase and so infected leaves might inadvertently be used in leaf disc tests. However, the effect of cocoa swollen shoot virus infection of leaves on the results of leaf disc test is not known. The objective of this study was to understand the effect of CSSV on leaf disc test to help select cocoa genotypes resistant to Phytophthora species. Leaf disc test with virus infected and healthy cocoa leaf tissues were therefore conducted to determine the effect of the virus infection on the results of leaf disc test. Significant differences were observed among the cocoa genotypes in resistance to Phytophthora species. Interaction between cocoa genotypes and Phytophthora species was not significant. However, cocoa genotypes x Phytophthora species x virus strains interaction was significant. Leaf discs from genotypes infected by CSSV were more resistant to Phytophthora species than those from healthy genotypes. The findings suggest that resistance of cocoa genotypes to Phytophthora species is significantly affected by CSSV and depend on the type of CSSV strain. Selecting and breeding for resistance to black pod disease using leaf disc test on cocoa genotypes with unknown CSSV status could be waste of time and resources. Care must therefore be taken in the collection of leaf samples to undertake leaf disc test especially in West Africa where the CSSV is prevalent. It is suggested that cocoa swollen shoot virus status of leaf samples be detected using CSSV diagnostic tools before using them for leaf disc test.