PCR-RFLP of three mtDNA regions ( srRNA gene ,irRNA gene and intergenic COI – COII region) were used to investigated the distribution of northern and southern Apis cerana populations of 89 colonies from Prachuap Khiri Khan and Chumphon provinces. Three, four and eight haplotypes were obtained from DraI digestion of PCR-amplified 410 bp srRNA gene, 755bp IrRNA gene and 1710 bp intergenic COI-COII region,respectively. These three mtDNA regions generated 11 composit haplotypes. Twelve composite haplotypes were generated when samples from Yunnan and Hanoi were included. A UPGMA phenogram based on genetic distance allocated A.cerana in these province into 2 distinct group: northern and southern. Their distribution areas had overlapped in Amphur Bang Sapan (Prachuap Khiri Khan ). Bang Sapan Noi (Prachuap Khiri Khan). Tha Sae (Chumphon) and Pa Thiu (Chumphon). Only one type of intermediate haplotype. BAB was found in the contact zone with low frequency indicated that northern and southern populations of bees in Thailand were colonized by separate population. The northern population of A.cerana in Thailand might be colonized by bee from Vietnam. Notably,private haplotype of all amplified regions were found from one sample in Prachuap Khiri Khan. The composite haplotype,CED,was extremely different from all samples having morphological similarity. It was suspected to be the other species. Further study is needed to be carried out to clarify their actual taxonomic status. Microsatellite DNA analysis of 4 geographic samples (1. Central, 2. South, 3. Prachuap Khiri Khan and 4.Chumphon ) was performed by using A.mellifera microsatellite primer. Three microsatellite loci (A28, A107, and A113) showed polymorphic. PCR products of loci A28 and A107 were very difficult to accurately score because of their stutter bands nature. The heterozygosities of A.cerana were estimated from microsatellite loci A113 was 0.451 - 0.550. The analysis of geographic differentiation indicated no differentiation of four geographics of A.cerana . Therefore, crossed mating of male bees in the contact zone (Prachuap Khiri Khan and Chumphon) might occurred.