The consequences of Quaternary climatic fluctuations on plant evolutionary history have been well documented in North America and Europe but have been far less studied in the Neotropical region. Diversification patterns in South American grasslands have been neglected, especially in the Pampas. In this study, we applied an ensemble-modeling framework and a bioregionalization method to test the hypothesis that Petunia axillaris subspecies responded differently to past climate changes in the South American grasslands. Scenarios for the future were projected to better understand the consequences of climatic shifts on the species’ survival. Our results revealed that each subspecies is currently distributed in different bioregions and displays substantial geographic separation as a consequence of past climate oscillations. The projected future scenarios suggest that all subspecies would be affected by habitat fragmentation. This could influence the genetic structuring among P. axillaris populations, as the diversity of grasslands species depends on the genetic characteristics of the remaining populations over the fragmented regions. These results reinforce the importance of considering intraspecific diversity when planning conservation efforts in grasslands in southern South America.