The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.

Aim  In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique evolutionary history, which is reflected by their genetic makeup. Location  Sub‐Saharan Africa and India, with special focus on West and Central Africa. Method  In this study 126 samples, throughout the lion’s complete geographic range, were subjected to phylogenetic analyses. DNA sequences of a mitochondrial region, containing cytochrome b, tRNAPro, tRNAThr and the left part of the control region, were analysed. Results  Bayesian, maximum likelihood and maximum parsimony analyses consistently showed a distinction between lions from West and Central Africa and lions from southern and East Africa. West and Central African lions are more closely related to Asiatic lions than to the southern and East African lions. This can be explained by a Pleistocene extinction and subsequent recolonization of West Africa from refugia in the Middle East. This is further supported by the fact that the West and Central African clade shows relatively little genetic diversity and is therefore thought to be an evolutionarily young clade. Main conclusions  The taxonomic division between an African and an Asian subspecies does not fully reflect the overall genetic diversity within lions. In order to conserve genetic diversity within the species, genetically distinct lineages should be prioritized. Understanding the geographic pattern of genetic diversity is key to developing conservation strategies, both for in situ management and for breeding of captive stocks.

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