Significance
Although today the rainforest is continuous in Central Africa, the scarce fossil record suggests that arid conditions during the ice ages might have reduced tree density. However, the vast majority of the fossil pollen cores preserved in Tropical Africa are too young to inform about this period. Investigating whether the climate change left a genetic signature on trees can thus be useful to date past forest fragmentation. We use DNA technology to study five legume trees. Our results show significant differentiation of the populations of each species at a date compatible with forest fragmentation driven by ice age climatic oscillations. Contrasted timescales were obtained for each species, in agreement with different recolonization abilities in an expanding forest biome after fragmentation.