<strong>Aim</strong> We sought to test the refuge hypothesis as a major driver of genetic differentiation to explain the development of distinct phytogeographical domains in tropical Central African rain forest. To address this aim, we studied the phylogeographical pattern of a pair of sister plant species, Haumania danckelmaniana and H. liebrechtsiana (Marantaceae), distributed across the two phytogeographical domains: Lower Guinea and Congolia. <strong>Location</strong> Tropical Central Africa including the phytogeographical domains Lower Guinea and Congolia. <strong>Methods</strong> Seven polymorphic microsatellite loci were genotyped in a total of 513 individuals from both species. The dataset was analysed for population genetic structure and demographic change and the results compared to the geographical pattern of plastid DNA sequences from a previous publication and other sympatric species. <strong>Results</strong> Based on the microsatellite dataset, three distinct homogeneous genetic clusters were detected in H. danckelmaniana and two in H. liebrechtsiana. These clusters corresponded geographically with the patterns found in the plastid DNA sequences. Genetic diversity and endemism were unevenly distributed between clusters in the two species. Most clusters exhibited signals of population expansion. <strong>Main conclusions</strong> The phylogeographical data based on microsatellites and plastid DNA revealed a complex history involving (1) allopatric differentiation with each species originating in a different phytogeographical domain, potentially resulting from past forest fragmentation, followed by (2) population expansion and interspecific introgression, which probably occurred during a phase of forest expansion. Moreover, phylogeographical patterns within each species provided evidence of (3) past population fragmentation followed by partial population admixture in H. danckelmaniana, and deep differentiation between Lower Guinea and Congolia in H. liebrechtsiana. The observed patterns were globally consistent with the refuge hypothesis and the presented scenario illustrates evolutionary processes that likely have contributed to shaping the African phytogeographical domains.< Réduire