<p>The unique characteristics of the Brazilian Atlantic Forest challenge integrative studies in biogeography, evolution, and taxonomy due to the distinctive genetic, morphological, and phylogeographic patterns observed in its species. The diversification of the Neotropical rodent <i>Akodon cursor</i> exemplifies these complexities. To better understand the biogeographical processes driving this diversification, we integrated genetic, ecological, and geographical perspectives to reevaluate the phylogeography of <i>A. cursor</i>. Our approach involved analyzing an extensive multilocus DNA sequence dataset, climatic niche models, and chromosomal features. We tested three primary hypotheses to explain species diversification within the heterogeneous Atlantic Forest: the Riverine Barrier Hypothesis, the Forest Refugia Hypothesis, and the Atlantis Forest Hypothesis. Our findings revealed a complex genetic structure within <i>A. cursor</i>, identifying three primary phylogroups across the northern, central, and southern regions of the forest. Contrary to expectations, rivers played a relatively minor or secondary role as geographic barriers for <i>A. cursor</i>. Instead, Quaternary glacial cycles emerged as the dominant force shaping the current diversity patterns of this species within the Atlantic Forest. Additionally, our study supports the Atlantis Forest Hypothesis, indicating that population expansions occurred during glacial cycles (cold-dry periods) and habitat fragmentation during interglacial cycles (warm-wet periods). While we did not find strong evidence for the subdivision of <i>A. cursor</i> into sibling species, our results suggest that this taxon is in the early stages of speciation. These findings underscore the value of <i>A. cursor</i> as an exemplary model for evolutionary studies within the Atlantic Forest.</p>