*Medical Science Programme, Faculty of Medicine, Chulalongkorn University
**Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Rama IV Rd, Patumwan, Bangkok 10330,Thailand.
***Department of Biochemistry Faculty of Medicine, Chulalongkorn University, Rama IV Rd, Patumwan, Bangkok 10330,Thailand.
****National institute of Health, Department of Medical Sciences, the Ministry of Public Health, Tiwanon Rd, AmphurMuang Nonthaburi 11000, Thailand.
*****Department of Parasitology, Faculty of Medicine, Chiang Mai University, Inthawarorot Rd, Sriphum, Muang, Chiang Mai 50200, Thailand
******Department of Dairy Science (Applied Entomology), Rakuno Gakuen University, 582 Midori Machi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan.
We demonstrated the using of the internal transcribed spacer (ITS2) of ribosomal DNA as a tool for identification of medically and veterinary important Muscidae flies in Thailand. A total of 27 fly samples were collected from various regions of Thailand. Six fly species in three subfamilies including Azeliinae (Hydrotaea spinigera), Muscinae (Musca domestica, M. sorbens) and Stomoxyinae (Stomoxys calcitrans, S. indicus and S. sitiens) were identified base on morphological taxonomy. PCR amplicons of the ITS2 gene of these flies varied between 312-377 bp with A+T content of 76.6%. ITS2 sequences of the flies in this study were 93-100% identity to sequences in database and 21 samples were compatible with morphological identification, while sequences of 6 samples did not match any sequences in the database. The intra- and inter-specific divergence analysis results showed that the maximum of intra-specific (within species) variation (6.9%) was found in M. domestica while the minimum inter-specific (between species) variation (11.9%) was found in the sister grouped couple of S. sitiens and S. indicus. No overlapping between intra- and inter-specific divergences was found in all species of this study. The bootstrapped NJ tree constructed showed ability to classify each subfamily in to monophyletic clades. PCR-RFLP using XapI restriction enzyme digestion was able to differentiate between the three Stomoxys species. Data obtained from this study would be valuable for both medical and veterinary entomologists for more accurate identification of important fly species. Therefore, it could be used for population dynamics studies and enrolled in integrated pest management control program.