The origin of bonobos and the history of their dispersion in the southern Congo Basin were investigated from the perspectives of biogeography and the paleo-environment. Why bonobos are distributed in the southern Congo Basin was unclear because of limited geological records about the region and genetic information for bonobos. Recently, colleagues and I proposed some hypotheses concerning the history of bonobos based on recent reports about marine sediments and structural geology of the Congo basin, as well as new mitochondrial DNA haplotypes collected from seven wild bonobo populations. Here, I illustrate these hypotheses, namely: 1) the Congo River functioned as a biogeographical barrier for forest animals since 34 million years ago; 2) the ancestor of present bonobo populations crossed the upper parts of the Congo River from the right bank to the left bank during the early Quaternary period; and, 3) factors affecting the genetic structure of present bonobos. Lastly, I propose possible future studies to investigate bonobo evolution.