Quantitative trait loci (QTL) mapping for agronomic traits was carried out in cocoa (Theobroma cacao L.). Regions of the genome involved in yield, vigor, and resistance to Phytophthora palmivora were identified. Three heterozygous clones, one upper Amazon Forastero (IMC78) and two Trinitario (DR1 and S52), were crossed with the same male parent, a lower Amazon Forastero (Catongo), known to be highly homozygous. Observations were made on progeny over nine consecutive years. One to three QTL related to yield were detected in each of the three populations, located on chromosomes 1, 2, 4, 5, 9, and 10. They explained between 8.1 and 19.3% of the phenotypic variation and showed various levels of repeatability. In IMC78, the QTL detected on chromosome 5 was the most repeatable over years. The QTL for the average individual pod weight on chromosome 4 was the most significant with an LOD of 17.3 and an R2 of 43.7. QTL related to these traits were identified in the same region of the genome in clones of different genetic groups. This suggests that molecular markers can be used to improve cocoa varieties.