Our integrative approach combines two mitochondrial genes (16S and cyt b gene), two nuclear genes (exon 10 GHR and exon 1 IRBP) and craniometrical data to test the status and to infer phylogenetic relationships of the three Praomys Cameroon Volcanic Line endemics (P. hartwigi, P. morio and P. obscurus). The taxonomic rank of the principal genus group is assessed and the mode of diversification of species of the P. tullbergi complex in Afrotropical forests is discussed based on estimates of times to the most recent common ancestors and on tree topologies. This study documents for the first time the molecular and morphometrical distinctiveness of P. hartwigi and P. morio within the P. tullbergi species complex. Further studies including specimens of P. hartwigi from all its distribution range are needed to conclude on the status of P. obscurus. The monophyly of the genus Praomys is refuted. Times to the most recent common ancestors of major clades within the P. tullbergi species complex are estimated for the last 2.5 Mya and during the last 1 or 2 Mya for different species or forms. The lowland forest refuge hypothesis might well explain the diversification of P. misonnei, P. rostratus and P. tullbergi in the guineo-congolese forest block. The isolation of montane forests could have facilitated the divergence between the two montane forest forms P. hartwigi and P. obscurus and between populations of P. morio from the continent and those from the island of Bioko. Praomys populations (species) that inhabit the Cameroon Volcanic Line Praomys probably originated as lowland forms subsequently specialized to highland conditions.