Abstract Camu-camu (Myrciaria dubia, Myrtaceae) has the highest reported vitamin C concentrations of any native Amazonian fruit tree species, with increasing demand in domestic and international markets. With the goal of aiding management and conservation programs, we studied the diversity of camu-camu in cultivated and uncultivated areas, based on physicochemical characterization of the fruits. We evaluated 2,250 fruits from 87 plants from six localities of the Tarapacá district (Amazonas, Colombia) and from the Amazonian fruit germplasm bank of Agrosavia (Meta, Colombia). We found high physicochemical variability within and among localities, and superior fruits in the localities where non-cultivated plants were sampled, especially Pechiboy. Using correlations and principal component analyses, we identified the variables Brix value, ascorbic acid content, fruit weight and pulp yield as the most useful for intraspecific selection of plants. The most promising plants presented Brix values of 8.2 ± 0.88 (maximum 10.9), fruit mass of 14.4 ± 1.2 g (max. 18.4 g) and pulp yields of 0.82 ± 0.02 (max. 0.87). These plants can be considered as possible sources for future breeding work. We conclude that there are plants in Tarapacá with relevant characteristics for commercialization and improvement of the species.