Endemic honey bees of the Tien Shan Mountains in Central Asia are described as a new subspecies, Apis mellifera pomonella, on the basis of morphometric analyses. Principal component and discriminant analysis of the morphological characters measured clearly place these bees into the oriental evolutionary branch of honey bees, but also show that they are distinct from the other subspecies in this lineage. The existence of this newly described honey bee subspecies extends the range of endemic A. mellifera more than 2000 km eastward than previously estimated. Sequence analysis of mitochondrial DNA places A. m. pomonella within the C mitochondrial lineage (a group that is inclusive of both C and O morphological lineages). These findings support the conclusion that A. m. pomonella has a phylogeographic history shared with subspecies from the eastern limit of the previously known range.