Background: Pleistocene climatic oscillations led to range fluctuations in African rain forest organisms. Isolation of populations during the driest climatic phases resulted in genetic differentiation through mutation and drift. Recent re-expansion of the forest brought differentiated groups into secondary contact. We investigated whether past climate changes may have led to sufficient differentiation to trigger speciation in a central African rainforest tree, Barteria fistulosa (Passifloraceae). Method: We genotyped 765 individuals of B. fistulosa at 12 microsatellite loci and characterized the spatial genetic structure by using Bayesian clustering algorithms, isolation-by-distance analyses and clines of synthetic alleles. We used species niche modelling (environmental and soil variables) to investigate ecological variables associated with genetic discontinuities. Results: Trees showed a very steep genetic discontinuity between groups north and south of latitude 1°N. There was no evidence for effective gene flow between the two tree lineages in contact at the transition zone, despite the presence of a few hybrids. Niche modelling did not predict the occurrence of northern trees south of this genetic transition, and vice versa. The variable that contributed the most to niche differentiation was precipitation during the driest quarter of the year. Discussion: The genetic discontinuity near latitude 1°N is inferred to be a tension zone resulting from reproductive incompatibilities between previously allopatric tree lineages. This tension zone may have stabilized at a climatic transition (between boreal and austral seasonal regimes), and matches patterns of genetic structure previously observed in other forest plant species of the region, suggesting that a tension zone may separate distinct lineages of several central African forest plants near the thermal equator. Our results suggest that northern and southern lineages could be locally adapted to climatic parameters,