Campomanesia is a well-circumscribed genus within Myrtaceae, but the boundaries among some of its species remain poorly understood. Microsatellite amplification profiles have proven useful DNA fingerprinting for plant species identification, but have never been applied to the taxonomy of this genus. Here we studied 12 species of Campomanesia, including a set of related and non-related species, as well as species with doubtful boundaries. Forty-eight morphological characters and 50 primers were used to test the species. A cluster analysis followed by a group sharpness test and a heat map analysis was performed with both sets of data. A regression tree was constructed using only on the molecular data. Seven groups based on morphological characters and five groups based on molecular characters were revealed by cluster analysis and the sharpness group test. The microsatellite amplification profiles were efficient at distinguishing the studied species, despite the smaller number of distinct groups formed by this marker compared with the morphological data. Among the 50 primers included, 13 were informative for species distinction, and 10 were indicated by the regression tree to species identification. Microsatellite amplification profiles proved to be an informative tool for the taxonomy of Campomanesia.