Abstract Despite vigorous genetic studies of African elephants ( Loxodonta africana and L. cyclotis) during the last decade, their evolutionary history is still obscure. Phylogenetic studies and coalescence time estimation using longer nucleotide sequence data from denser samplings are necessary to better understand the natural history of African elephants. Further, species identification among African elephants is sometimes very difficult using only the external morphological characteristics. This is a serious problem for making an adequate breeding plan in zoological gardens. In this paper, we investigated the continent-wide phylogeographical pattern of the African elephants and estimated the coalescence times among them. From these molecular data and geological evidence, we proposed an evolutionary scenario for the African elephants. We further demonstrated the effectiveness of molecular phylogenetic methods in species identification.