In south India there are two distinct colour morphs of cavity nesting honey bees: the yellow Plain morph and the black Hill morph which are collectively known as Apis cerana. We show that the Hill morph is associated with a widely distributed mitochondrial haplotype that is present throughout mainland populations of south east Asian A. cerana. In contrast, the Plain morph, which is apparently confined to low to moderate elevations in India and Sri Lanka, is associated with a unique mitochondrial haplotype that is not present in other cavity nesting honey bees. We further show that in a region of sympatry (Bangalore, Karnataka State) the drone mating flight times of the two colour morphs barely overlap. Combined, drone flight data and the complete separation of mitochondrial haplotypes suggest that the two morphs are reproductively isolated. The Plain morph is distinguished from the Hill morph by the first three abdominal tergites of the worker, which are completely yellow in the Plain morph, whereas in the Hill morph they are black or black with yellow patches. Although the two morphs are generally distinguishable in the field by overall colouration, microscopic examination of the first 3 abdominal tergites is preferred.