Tropilaelaps spp. are ectoparasitic bee mite naturally infesting on Apis dorsata (Ad) colonies that distribute in Thailand. Recent report is identified into T. mecedesae which is important wide destroying in A. mellifera (Am) colonies in the world. Tropilaelaps populations of Thailand were analyzed by using morphometric, geometric and genetic variation at COI and ITS genes. All 6 morphometric characters and 30 geometric landmarks of Tropilaelaps were measured by using tpsDig2.16 from images. All morphological characters of mite populations infesting on A. dorsata could be bigger than A. mellifera but they were not statistically significant. All of mite populations showed same characteristics that resembled to T. mercedesae. And geometric method were supported by the scatter plots of relative warp analysis concluded that Tropilaelaps populations could be similarity in Thailand. Moreover, both of morphological methods showed diversity in characters of mite anal shield which was a key character of Tropilaelaps identification. In part of COI and ITS genes variation of mite populations were determined by PCR-RFLP and sequencing. Most of samples were detected T. mercedesae about 94.34% and T. koenigerum about 5.6% infesting on A. dorsata colonies also about 100% T. mercedesae infesting on A. mellifera colonies. The 538 nucleotides of COI gene sequences showed percentage of A+T higher than G+C. The mite sequences from Thailand selected into 5 sequences (3 from Ad and 2 from Am) compared with 18 sequences from different distribution area in Asia. The multiple sequences were aligned and calculated phylogenetic relationship using maximum parsimony, minimum evolution, neighbor-joining and UPGMA assumption in MEGA 4.0. The relationship of 23 Tropilaelaps sequences showed 2 newly haplotypes, TmThailand3 and TmThailan4, those could be ancestor of T. mercedesae. One haplotype of T. koenigerum was newly report into TkThailand1, which all three haplotypes found in A. dorsata colonies. But, haplotype of Tropilaelaps infested A. mellifra was as same as TmThailand1 and TmThailand2 in database. The results suggested that Tropilaelaps populations of Thailand might be contract population of T. mercedesae and T. koenigerum of Mainlan Asia.