The rodent Deltamys kempiThomas, 1917 is found on the Coastal Plain – a recently formed geographic region located on Brazil’s south-east coast. Considering that Deltamys is the only South American sigmodontine with a sex chromosome system of type X1X1X2X2/X1X2Y, this investigation was focused on the phylogeographic history of this taxon by using gene sequence analysis, trying to clarify when Deltamys differentiated, what was its centre of diversification, and what were the probable routes it used to reach its present distribution. We analysed sequences of the mitochondrial cytochrome b gene and nuclear recombination activating gene 2, performed cranial measurements and searched for centric fusions in individuals collected in distinct localities. The results, clearly demonstrate that D. kempi, on the Coastal Plain, divided into two groups, one occupying a small portion to the north of this region and the other spreading widely to the south. In this process, the phenomena of marine transgression and regressions which moulded its habitat, together with the occurrence of successive chromosomal rearrangements, were certainly the fundamental factors in shaping D. kempi diversification.