Introduction: The ex situ conservation and characterization of native Theobroma cacao L. genetic resources are critical for sustainable cacao production and breeding programs in the face of climate change and escalating disease pressures. This study aimed to establish and characterize a novel germplasm bank from the Loreto region of the Peruvian Amazon, a key center of cacao diversity. Methods: We collected 140 native cacao accessions across 15 river basins in eight provinces of the Loreto region. Accessions were propagated using optimized grafting techniques with IMC 67 rootstock. Phenotypic evaluation was conducted on 402 plants using 36 standardized descriptors (25 quantitative and 11 qualitative). Data analysis included multivariate analysis using Uniform Manifold Approximation and Projection (UMAP) and Shannon-Weaver diversity indices to assess morphological diversity patterns. Resu...