Myrtaceae species play an important role in maintaining the biodiversity of the Atlantic Forest. However, most species of this biome have not been studied. In this work we examined whether microsatellite markers developed for other Myrtaceae species are useful in genetic studies of native species of the Atlantic Forest. We evaluated the transferability of 21 microsatellite markers derived from Eucalyptus sp., Eugenia uniflora, and Melaleuca alternifolia Cheel to eight Atlantic Forest species (Campomanesia xanthocarpa (guabiroba do mato), Campomanesia adamantium, Eugenia uniflora (surinam cherry), Eugenia involucrata (cherry of the Rio Grande), Myrcianthes pungens (guabiju), Plinia cauliflora (jaboticaba), Psidium guajava (guava), and Psidium sp.(araçá) and the utility of the transferred markers in obtaining genetic data from Eugenia uniflora. The transferability of microsatellite primers pairs was high (>52%) in seven of the eight species studied. In three populations of E. uniflora, the transferred primers amplified the same average number of alleles, and the same expected heterozygosity was obtained with species-specific primers. The genetic parameters F_IS, Shannon diversity, genetic distance of Nei, F_ST and F_IT, AMOVA, and the PCoA were calculated using data from four transferred microsatellites. Results were similar to those obtained using species-specific primers. Both datasets (from transferred and species-specific primers) indicated that E. uniflora populations of the Atlantic Forest are unstructured and have high genetic diversity. The results of our study indicate that transferability of microsatellite markers is an economic and powerful way to obtain genetic information of Myrtaceae species of the Atlantic Forest, and consequently, will aid in the conservation of these species and the biome.