Phytophthora pod rot (PPR) caused by the specie Phytophthora megakarya is an important disease of cacao tree. Association mapping identified markers linked to PPR resistance in a cacao population of 260 trees planted under high disease pressure in a single plantation in a farmer's field. These cacao trees were derived from both selfing and full-sib progenies. The resistance traits were assessed through field observations of the natural pod attacks of the disease on the trunk (PRTnk) or the canopy (PRCpy) of cacao trees (expressed as the percentage of PPR-infected pods), and the development of the symptoms on the pods two (PT2d) or five days (PT5d) after artificial inoculations. A total of 108 SSRs markers loci covering the 10 chromosomes of the cacao genome were used in the analysis. The percentages of admixture of each genotype, estimated using 17 neutral SSRs markers, were used as co-factor in the analyses, decreasing the proportion of false-positive due to population structure. General and mixed linear models were used to analyze phenotypic data collected over 3 years. For field PPR incidence and artificial pod inoculation tests, a total of 36 and 18 individual marker-trait associations were detected, respectively. The positive and significant correlations found between PT5d and field measurements (PRTnk and PRCpy) explained the fact that both traits were co-localized with PPR scores in 9 marker-trait associations. The results of this study highlight the interests of association mapping to decipher the PPR genetic control and to guide the breeding strategies to produce a sustainable cacao resistance to Phytophthora species.