DNA sequence diversity in the tRNA(leu)-COII portion of the mitochondrial genome was investigated in samples of Apis cerana from Yunnan, China. A fragment of about 480 bp in tRNA(leu)-COII, including a noncoding area and part of COII, was sequenced. The noncoding area was 97-98 bp; 8 haplotypes were found, among which 5 had been reported previously, while 3 were new. The mean diversity of haplotypes was 0.752 ± 0.030 (0.378-0.698), and nucleotide diversity was 0.01073 ± 0.00087 (0.00412-0.01123). A neighbor-joining tree was constructed based on 73 sequences of noncoding intergenic regions in the mtDNA of A. cerana from China and other Asian countries; all haplotypes found in China fell into the mainland Asian group. This result does not support the hypothesis that A. cerana indica occurs in southern Yunnan, which was concluded in a recent report based on morphological variation.