The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic are taxonomically problematic, as they are referred to as either peralta, or antiquorum, or congoensis. In this study, a mitochondrial fragment of 1765 nucleotide sites, covering the complete cytochrome b gene, three transfer RNAs and a large part of the control region, was sequenced to assess the relationships between several populations of giraffe. The phylogenetic analyses performed on the 12 identified haplotypes indicate that northern giraffes constitute a natural group, distinct from that of southern giraffes. Surprisingly, the giraffes of Niger are found to be more closely related to the giraffes of East Africa (subspecies rothschildi and reticulata) than to those of central Africa. We conclude therefore that the subspecies peralta contains only the Niger giraffes, whereas the subspecies antiquorum includes all populations living in Cameroon, Chad, the Central African Republic, and southwestern Sudan. We suggest that the ancestor of the Nigerian giraffe dispersed from East to North Africa during the Quaternary period and thereafter migrated to its current Sahelian distribution in West Africa, in response to the development of the Sahara desert. This hypothesis implies that Lake Mega-Chad acted as a strong geographical barrier during the Holocene, preventing any contact between the subspecies peralta and antiquorum. Our study has direct implications for conservation management, as we show that no subspecies peralta is represented in any European zoos, only in Niger, with a small population of less than 200 individuals.