Camu – camu, Myrciaria dubia (Myrtaceae) is a native species of the Amazon Rainforest that has been attracting attention worldwide and arousing great interest in the food and pharmacological industries due to the high concentrations of ascorbic acid in its fruit, which is exported to several countries. Characterizing different materials of M. dubia by means of molecular markers allows integration of agronomic and molecular information to aid in the search for more promising varieties. We examined the genetic variability of 11 populations of this species distributed along the Branco River hydrographic basin in state of Roraima in northern Brazil. The populations were defined taking into account the origin of the subsample. The 55 sub-samples present in the Embrapa Roraima Germplasm Collection were evaluated using five ISSR initiators (UBC 811, UBC 812, UBC 817, UBC 868 and UBC 880). The five primers tested generated 64 fragments, with a 98% polymorphism rate. The greatest genetic variation was expressed within the populations (66.6%), while the lowest divergence was determined among the populations (33.4%) of the collection. There was a significant correlation between genetic and geographical distances (Mantel test, r = 0.3%, P < 0.01). Analysis with the UPGMA method gave four subgroups showing that various individuals are genetically divergent and can be used in genetic breeding programs.