The spatial and genetic distribution analysis and the anatomical knowledge of a species is a very useful tool to understand your ecological behavior because it provides information that underlie management strategies and influence the population structure. The present study aimed to study the horizontal structure of the species Theobroma speciosum (cacauhy) and Theobroma subincanum (cupui) and also characterize the genetic diversity and anatomy of leaves of T. speciosum, recording the structural differences observed between sun leaves and shade leaves. The genetic diversity detected was spatially structured within the population, and that the closer the trees, more is the probability of being closely related. In relation to spatial distribution, the T. speciosum individuals showed aggregated distribution pattern, while T. subincanum presented a random pattern. The diameter distribution of T. speciosum followed a distribution in the form of inverted "J", behavior expected for a forest environment with low anthropic pressure, as T. subincanum not followed the same pattern, however the species proved to be well established in the area, with a significant number of individuals in all diameter classes. The constitution of the sun and shade leaves of T. speciosum mesophyll varied with the environment. Plants exposed to full sunlight showed longer cells in the palisade parenchyma, spongy parenchyma also showed many layers of overlapping cells, whereas shade leaves showed cells with many intercellular spaces. Were observed significant anatomical changes caused by variations of light intensity on the leaves, which revealed a large adaptive capacity of T. speciosum. Thus, the results indicate the importance of conservation areas established in order to safeguard the natural environment from the pressures of different anthropic actions, and also the need for studies in the region of the Amazon biome.