This study adds new data from Korea and the Philippines to earlier mitochon
drial DNA (mtDNA)-based studies of the phylogeography of Asian cavity-nesti
ng honeybees. A non-coding region that lies between the leucine tRNA gene a
nd the cytochrome oxidase II gene of the mitochondrial genome was sequenced
in bees from 153 colonies of Apis cerana and A. nigrocincta, revealing 41
different haplotypes. Five sequences could not be aligned with the others,
two (from India and Sri Lanka) because the sequences were exceedingly A+T r
ich, and three (from Taiwan, the Philippines, and A. nigrocincta) because m
ost of the non-coding sequence was absent. The remaining 36 sequences were
aligned, and used in a phylogenetic analysis of A. cerana and A. nigrocinct
a populations. Both neighbor-joining and parsimony analyses were carried ou
t, yielding similar results. We found five major groups of haplotypes: an A
sian mainland group, a Sundaland group, a Palawan group, a Luzon-Mindanao g
roup, and A. nigrocincta. The geographic distribution of these mtDNA haplot
ypes appears to be strongly influenced by changes in sea-level during Pleis
tocene glaciations.