BackgroundQuaternary climatic changes led to variations in sea level and these variations played a significant role in the generation of marine terrace deposits in the South Atlantic Coastal Plain. The main consequence of the increase in sea level was local extinction or population displacement, such that coastal species would be found around the new coastline. Our main goal was to investigate the effects of sea level changes on the geographical structure and variability of genetic lineages from a Petunia species endemic to the South Atlantic Coastal Plain. We employed a phylogeographic approach based on plastid sequences obtained from individuals collected from the complete geographic distribution of Petunia integrifolia ssp. depauperata and its sister group. We used population genetics tests to evaluate the degree of genetic variation and structure among and within populations, and we used haplotype network analysis and Bayesian phylogenetic methods to estimate divergence times and population growth.ResultsWe observed three major genetic lineages whose geographical distribution may be related to different transgression/regression events that occurred in this region during the Pleistocene. The divergence time between the monophyletic group P. integrifolia ssp. depauperata and its sister group (P. integrifolia ssp. integrifolia) was compatible with geological estimates of the availability of the coastal plain. Similarly, the origin of each genetic lineage is congruent with geological estimates of habitat availability.ConclusionsDiversification of P. integrifolia ssp. depauperata possibly occurred as a consequence of the marine transgression/regression cycles during the Pleistocene. In periods of high sea level, plants were most likely restricted to a refuge area corresponding to fossil dunes and granitic hills, from which they colonized the coast once the sea level came down. The modern pattern of lineage geographical distribution and population variation was established by a range expansion with serial founder effects conditioned on soil availability.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0363-8) contains supplementary material, which is available to authorized users.