Our recent phylogeographic study on the strictly savanna small rodent Nannomys minutoides revealed an unexpected pattern of divergence between populations occupying neighbouring savanna islands in Central Gabon, suggesting the historical and continuing fragmentation of these savanna habitats. In this study, we test this hypothesis using comparative phylogeography with another species of savanna rodent, Lemnhcomys striatus, using nested clade analysis (NCA) on cytochrome b sequences of 53 individuals, particularly checking for vicariance patterns in the Lopé National Park region. Lemniscomys striatus is characterized by a local structured pattern similar to that of N. minutoides. These new results further support the scenario of historical and ongoing fragmentation of the local savanna landscape which commenced in the upper Pleistocene, despite the repetitive savanna expansion episodes as documented by the landscape history. Geographic barriers most likely comprising forested areas, which prevent the mixing of local savanna rodent populations, must have persisted in this region. The presence of these barriers could not have been inferred from global paleoclimatic and paleoenvironmental analyses alone.