Abstract:The quantification of genetic diversity and intrapopulation spatial genetic structure (SGS) of tree species are important aspects for in and ex situ conservation practices. In this study we seek to understand the importance of conservation areas by quantifying the genetic diversity and the spatial genetic structure of a natural population of Theobroma speciosum. Within this population, 49 adults and 51 subadults were genotyped for five microsatellite loci. The results showed that adults and subadults have similar levels of genetic diversity and inbreeding (adults: A= 10.4, A e = 10.3, F= 0.68, subadults: A= 10.6, A e = 10.6, F= 0.57). Genetic diversity was spatially structured within the population, and the results suggest that near-neighbor trees up to a distance of 70 m are likely related. SGS is likely the result of short-distance seed dispersal, the short-distance range of pollinators, and infrequent breaches of the self-incompatible mating system. Considering the high demographic density of the species and size of the study area, as well as the high average number of alleles per locus and the presence of rare alleles, we believe that the study population is an excellent resource for in situ genetic conservation of T. speciosum. The study area is also a useful resource for collecting germplasm for ex situ conservation and seed collection, either for breeding programs used in the restoration of degraded areas or forest improvement. Rev. Biol. Trop. 64 (3): 1091-1099. Epub 2016 September 01.Key words: Amazonia, genetic variability, microsatellite markers, cacauhy.The national program of biological diversity, that evaluated and identified priority areas for conservation, sustainable use, and benefitsharing of biodiversity of the Brazilian Amazon, established 27 ecoregions of the Brazilian Legal Amazon (PNJU, 2013). One ecoregion is the Mato Grosso dry forests located in the Northern part of Mato Grosso State. In this area, the Juruena National Park (Parque Nacional do Juruena) was established in 2006 with the aim of protecting endemic Amazonian species. The Conservation Unit (CU) includes headwaters and stretches of important Amazonian rivers, such as Aripuanã, a tributary of the Madeira, Juruena, and Teles Pires Rivers, and tributaries of the Tapajós, and it encompasses an area of significant biogeographical interest. The genus Theobroma occurs naturally in the area.Several species within the Theobroma genus have conventional or potential uses, including Theobroma speciosum Willd. ex Spreng, commonly known as cacauhy. This species is important because it represents a possible source of genetic resistance for other, more economically important species, such as Theobroma cacao (Silva et al., 2011). The fruit rind of T. speciosum is mixed with wood ash to produce a handmade soap that is used in the Amazon and it is an excellent deodorant (Di Stasi & Hiruma-Lima, 2002). In relation to its fatty acids, Gilabert-Escrivá et al. (2002) noted that the composition is very similar to that found in cocoa butter. ...