Worldwide studies on Apis cerana variation for biogeography and genetic diversity depended largely on a 86~93 bp-long mitochondrial non-coding region (internal spacer region) located between tRNALeu and COII (named as NC2), possibly due to higher variability among available markers. In order to incorporate the A. cerana occurring in South Korea into world extensive data, we also sequenced the NC2 from 118 A. cerana samples collected over nine Korean localities and 66 A. cerana samples over seven Asian localities, such as China, Vietnam, and Thailand. These data were combined with preexisting world data to scrutinize genetic relationships of A. cerana in South Korea to outside distributional range. Sequencing of 184 samples provided a total of ten haplotypes: five from Korea, six from China, one from Vietnam, and two from Thailand. Among them eight were new, whereas two were previously reported ones. Phylogenetic analysis of A. cerana NC2 haplotypes so far found including ours has confirmed the presence of four major groups of A. cerana (Asian mainland group, Sundaland group, Palawan group, and Luzon-Mindahnao group) and all haplotypes found in this study also were included in the Asian mainland group. In order to find further variable regions that can be used as sequence-based marker several mitochondrial non-coding regions and nuclear intron regions are in the middle of testing.