This paper presents a quantitative vegetation reconstruction, based on a biomization procedure, of two mountain sites in the west (Bambili; 5°56′ N, 10°14′ E, 2273 m) and east (Rusaka; 3°26′ S, 29°37′ E, 2070 m) Congo basin in equatorial Africa during the last 18,000 years. These reconstructions clarify the response of vegetation to changes in climate, atmospheric pressure, and CO₂ concentrations. Two major events characterize the biome changes at both sites: the post-glacial development of all forest biomes ca. 14,500 years ago and their rapid collapse during the last millennium. The rates of forest development between the biomes are different; a progressive expansion of lowland biomes and an abrupt expansion of montane biomes. The trends of pollen diagrams and biome affinity scores are not always consistent in some periods such as the Younger Dryas interval and end of the Holocene Humid Period, because the biomization method is not a simple summarization of the pollen data, but also takes biodiversity into consideration. Our sensitivity experiment and inverse-vegetation modeling approach show that changes in atmospheric CO₂ concentration unequally influence vegetation in different local environments. The study also suggests that the biome changes prior to the Holocene result from both changes in the atmospheric CO₂ concentration and climate. The development of warm-mixed forest from xerophtic vegetation results from increases in atmospheric CO₂ concentration and near-surface air temperature. Difference in local dryness results in the different biome distributions, with more forest-type biomes at Bambili and more grass/shrub-type biomes at Rusaka.