The presence of vegetation corridors in fragmented landscapes has high ecological importance to the gene flow of animals and plants. The landscape in the south of Minas Gerais State, Brazil is characterized by fragmented and disturbed ecosystems. However, there is some secondary vegetation corridors connected with remaining fragments of primary forest. In order to obtain information regarding of the importance of vegetation corridors in maintaining genetic diversity, we assessed the genetic diversity parameters of Myrcia splendens in a fragment–corridor system. Inter-simple sequence repeat markers (ISSRs) were used to assess the genetic diversity and genetic structure of M. splendens. The genetic structure was constructed using 168 trees distributed in five forest fragments and 104 trees distributed in four vegetation corridors. High genetic diversity of the species was indicated by Nei and Shannon indices in the fragments (H E = 0.37, I = 0.53) and in the corridors (H E = 0.33, I = 0.48). The historical gene flow was higher with neighboring corridors than with non-neighboring corridors. Differentiation among fragments was observed to be low with no correlation between genetic and geographic distances (r = 0.057, P = 0.43). Our results indicate that the fragment-corridor system in Minas Gerais State, Southeast Brazil, analyzed is of great importance for M. splendens in situ conservation plans.