We studied the phylogeographical structure of Praomys misonnei (Rodentia: Muridae) in west-Central Africa based on 113 individuals from 31 localities and the sequencing of two mitochondrial genes (Cytb and CO1). Two clades can be identified through maximum likelihood, bayesian and network analyses: the first one is limited to the Korup National Park, while the second one has a broad geographical distribution in west-Central Africa. The second clade can be further divided into three sub-clades. The results of neutrality tests and mismatch distributions indicate that a population expansion occurred in these sub-clades. During the middle or upper Pleistocene, the west-Central African populations of P. misonnei may have been isolated in four different forest refugia, followed by population expansion and secondary contact during more humid periods. High genetic diversity was observed in the region of the Bakossi highlands, and the Cameroon Volcanic Line limits the geographical distribution of clades. Thus it seems likely that this volcanic line has in the past constituted a barrier that prevented the east—west exchange between P. misonnei populations through the expansion of the montane forest habitat. Our results also highlight the role of the Sanaga and Ogooué-Ivindo rivers in shaping P. misonnei genetic structure.