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Phylogeographic studies of tropical and subtropical tree species provide an ideal method to study the role of forest refugia in the structuring of genetic diversity in contemporary populations. To date, most studies have examined rainforest-dependent trees, yet the influence of forest refugia on savannah forest and woodland trees remains poorly understood despite their potentially important role in forest assemblages during the last glacial maximum. Here, we examine the level and structuring of genetic diversity across the geographic range of the savannah woodland tree, Khaya senegalensis-African mahogany, from Senegal to Uganda (>5000 km) and from the steppes of the Sahara desert to the fringes of Africa’s equatorial rainforests (700 km). Three chloroplast (cpDNA) loci and 13 nuclear microsatellite (nSSR) loci were genotyped in 503 individuals. Individual-based clustering of nSSR genotypes identified that all samples formed two populations that showed no pattern of geographic structuring. Population level analysis of nSSR data revealed only very weak genetic structure (F-ST=0.013) with most of the genetic diversity contained within populations. Geographical differentiation (G(ST)=0.096) was low for the 14 haplotypes identified. However, whereas all haplotypes occurred in the western populations (including Cameroon), only two cosmopolitan haplotypes were found in central-eastern populations. Geographically restricted low-frequency haplotypes were found in eight western populations. Higher genetic diversity in western populations was confirmed by patterns of allelic richness, which were lower in central-eastern populations. Taken together, these results indicate that K. senegalensis displays very little genetic differentiation across its geographic range and that previously identified barriers to dispersal across the northern savannah belt of tropical Africa (e.g. the Dahomey Gap, Mega Lake Chad and the Adamawa Highlands) have not impeded contemporary gene dispersal in this species. Nevertheless, clustering of rare haplotypes indicates that the Dahomey Gap has likely been an important historical barrier to genetic connectivity between western and eastern regions of the species and that it is likely that this savannah tree also experienced range contraction around major forest refugial fringes or riparian incursions during the last glacial maximum (LGM).