Recent discovery of an abundant and diverse late Miocene fauna at Toros-Ménalla (Chad, central Africa) by the Mission Paléoanthropologique Franco-Tchadienne provides a unique opportunity to examine African faunal and hominid evolution relative to the early phases of the Saharan arid belt. This study presents evidence from an African Miocene anthracotheriid Libycosaurus, particularly well documented at Toros-Ménalla. Its remains reveal a large semiaquatic mammal that evolved an autapomorphic upper fifth premolar (extremely rare in Cenozoic mammals). The extra tooth appeared ≈12 million years ago, probably in a small northern African population isolated by climate-driven fragmentation and alteration of the environments inhabited by these anthracotheriids [Flower, B. P. & Kennett, J. P. (1994) Palaeogeogr. Palaeoclimatol. Palaeoecol. 108, 537-555 and Zachos, J., Pagani, M., Sloan, L., Thomas, E. & Billups, K. (2001) Science 292, 686-693]. The semiaquatic niche of Libycosaurus, combined with the distribution and relationships of its late Miocene species, indicates that by the end of the Miocene, wet environments connected the Lake Chad Basin to the Libyan Sirt Basin, across what is now the Sahara desert.