Abstract
Cacao is a strategic crop in Peru due to its significant socioeconomic impact, driving extensive efforts to collect, characterize, and conserve its genetic diversity. This study aimed to establish phenotypic criteria to differentiate and structure the Cacao Amazonas Perú (CAP) germplasm, thereby providing a foundation for selection and breeding programs. A total of 113 accessions from the INIA Germplasm Bank were evaluated over two consecutive growing seasons using 33 quantitative and 18 qualitative agromorphological descriptors. Data were analyzed through univariate and multivariate approaches. The results revealed substantial phenotypic variability, with coefficients of variation reaching up to 37.5% for fruit-related quantitative traits, all exhibiting high heritability values (>60%). Principal component analysis indicated that the first two components explained 29.3% of the total variance, primarily influenced by fruit and seed descriptors. Hierarchical clustering analysis identified eight phenotypic groups; one cluster exhibited high seed mass and a favorable pod index (17.63), while another showed the highest seed index (1.55 g) and the greatest intragroup distance (7.54). This comprehensive characterization highlights accessions with superior agronomic and bioactive potential, providing a robust framework for parental selection, core collection development, and targeted breeding strategies to enhance cacao competitiveness and resilience under changing climatic conditions.