Morphometric characteristics combined with genetic markers are powerful tools used for determining honey bee subspecies. Bees samples collected from 94 established apiaries distributed throughout all of the Republic of Benin were morphometricaly characterized using seven parameters and the COI-COII regions of mitochondrial DNA were sequenced. Based on the morphometric data the native honey bees could be divided into three distinct ecotypes - the Benino-dry-tropical-ecotype in the north, the Benino-Sudanian-ecotype in the central part and the Benino-Sudano-Guinean-ecotype in the south. The DNA COI-COII regions sequence analyses confirmed that the honey bee population of the Republic of Benin belongs to different mitotypes but do not correspond with the determined ecotypes. We could determine three new haplotypes which missed the P0 segment but the Q region was duplicated or triplicated. Phylogenetic analyses clustered them together in the A evolutionary lineage. In conclusion, morphometric and genetic analysis of the native West African honey bees indicated that each of the different mitotypes was able to adapt to the different ecological conditions in the country by morphometric adjustments.