The diversity and genetic structure of natural populations are affected by several factors including migratory capacity, mating systems, ecological characteristics of their habitats, altitude, and recent and historical events . In A. flaccida the altitude was not considered because the populations of Xanxerê (777 m) and Marialva (700 m) are at similar altitude to Coxilha (750 m) and were still genetically distant. The analysis of the current ecosystems over the last 100 years and the history of these regions since the last glacial maximum led us to two complementary hypotheses for the diversity and genetic structure observed in A. flaccida populations.