The African lion (Panthera leo) is listed as vulnerable by the IUCN Red List, mainly threatened by indiscriminate killing, primarily as a result of retaliatory or pre-emptive killing to protect human life and livestock, and prey base depletion. Habitat loss and conversion has led to a number of subpopulations becoming small and isolated. With the weakened connectivity between the main strongholds, genetic drift and loss of genetic diversity could affect the genetic health of the species. In the present study, we investigated the evolutionary history of the species at different scales of time and space. A total of 182 samples were used, including a larger number of 77 samples from Tanzanian protected areas. The mitochondrial cytochrome b gene was sequenced and the specimens were genotyped for 11 microsatellites and more than 9,000 SNPs. The preliminary results indicate that the lion is structured into two lineages at the continental scale (West-Central vs South-Eastern), a pattern observed within many other large African savanna species displaying large distribution ranges. Pleistocene climatic oscillations and biogeographical barriers were proposed as the main factors to have driven the lineage sorting. The first results based on microsatellites highlighted that the Tanzanian population displayed good level of genetic diversities with no signs of inbreeding. Indication of isolation-by-distance nevertheless highlighted a potential future impact of fragmentation on the population genetic health. SNPs allowed to identify 3 populations of lions in Tanzania, geographically structured. Using various molecular markers, the present work will further explore the taxonomy and the evolutionary history of the African lion for bringing insights in its conservation requirements.