The boky-boky, Mungotictis decemlineata, is an endemic and presumed forest-dependent carnivoran species restricted to lowland central western Madagascar. It inhabits dry deciduous forests, which have been severely reduced in surface area with ∼60% destroyed or degraded by humans during the past 60 years. M. decemlineata is limited to the remnant forests of the central and southern Menabe, and using samples collected from sites across this zone, a phylogeographic study was conducted based on two mitochondrial (1140 base pairs [bp] of cytochrome b and 563 bp of the control region) and one nuclear fragment (591 bp of the seventh intron of the fibrinogen gene). Forty-seven individuals were included from the central Menabe from four principal localities and two animals from the southern Menabe from a single locality. Low sequence divergence (1.65% for the combined fragment, 4.26% for the control region and 0.78% for cytochrome b) characterized specimens across a zone of 130 km delimited by the Tsiribihina River to the north and the Mangoky River to the south; this area includes most of the geographical range of M. decemlineata. Phylogenetic trees, haplotype networks and exact test of population differentiation did not reveal any meaningful geographic partitioning of genetic variation. However, shallow yet significant genetic structure was revealed by ΦST calculations for the combined as well as separate DNA fragments, which we ascribe to isolation-by-distance. We proposed two different scenarios to explain the lack of meaningful phylogeographical structure in Mungotictis: (1) for this forest-dependent species, dispersal during periods of more continuous forest cover gave rise to a genetic meta-population or (2) that it is able to cross non-forested zones and broadly disperses, leading to high levels of genetic homogeneity. Current inferences favour the first hypothesis. The short- and medium-term future of this taxon is in jeopardy associated with habitat destruction across its geographical range.