The history of the genus Pan is a topic of enduring interest. Chimpanzees (Pan troglodytes) are often divided into subspecies, but the population structure and genetic history of chimpanzees across Africa remain unclear. Some population genetics studies have led to speculation that, until recently, this species constituted a single population with ongoing gene flow across its range, which resulted in a continuous gradient of allele frequencies. Chimpanzees, designated here as P. t. ellioti, occupy the Gulf of Guinea region that spans southern Nigeria and western Cameroon at the center of the distribution of this species. Remarkably, few studies have included individuals from this region, hindering the examination of chimpanzee population structure across Africa. Here, we analyzed microsatellite genotypes of 94 chimpanzees, including 32 designated as P. t. ellioti. We find that chimpanzees fall into three major populations: (i) Upper Guinea in western Africa (P. t. verus); (ii) the Gulf of Guinea region (P. t. ellioti); and (iii) equatorial Africa (P. t. troglodytes and P. t. schweinfurthii). Importantly, the Gulf of Guinea population is significantly different genetically from the others, sharing a last common ancestor with the populations in Upper Guinea ∼0.46 million years ago (mya) and equatorial Africa ∼0.32 mya. Equatorial chimpanzees are subdivided into up to three populations occupying southern Cameroon, central Africa, and eastern Africa, which may have constituted a single population until ∼0.10-0.11 mya. Finally, occasional hybridization may be occurring between the Gulf of Guinea and southern Cameroon populations.chimpanzees | phylogenetics | population biology | microsatellites R evealing the histories of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) is of widespread and enduring interest due to their close relationship with humans. A recent proliferation of research shows that we are just beginning to unravel their complex histories (1), and even now, we still debate the number of species and subspecies belonging to the genus Pan. Most authorities agree that chimpanzees and bonobos should be classified as different species, with their ranges separated by the Congo River ( Fig. 1; ref. 2). Chimpanzees are frequently further divided into subspecies across tropical Africa (2, 3), but this classification is disputed (4). P. t. verus occupies the Upper Guinea region of western Africa (2, 3). The range of P. t. troglodytes extends through central Africa. P. t. schweinfurthii occupies eastern Africa (2, 3) and has been proposed to be split into two subspecies, P. t. schweinfurthii and P. t. marungensis, based on craniometric variation (5).The subspecies name P. t. ellioti (6), formerly P. t. vellerosus (7, 8), has been proposed for chimpanzees from the Gulf of Guinea region, which spans southern Nigeria and western Cameroon (9). However, relatively little is known about the genetic history of chimpanzees from this region, and some question their distinctiveness from adjacent populations (4). Ana...