Log coffin burial practice is a unique late Prehistoric culture in Highland Pang Mapha, Mae Hong Son Province, northwestern Thailand within the documented a long-term occupation of the region, extending from the Late Pleistocene onwards. An important question is “who were the people that buried their dead in Log Coffins?” This paper addresses the question of whether Log Coffin populations were the descendants of the Late Pleistocene foragers of Highland Pang Mapha or new comers who migrated from elsewhere. Previous studies have compared ancient mitochondrial genomes of northern Thailand and southern China. The results showed limited maternal genetic connection between the two regions. However, there is still a paucity of ancient DNA study in Thailand compared with China. Here, we report on mitochondrial genomes from additional burial samples from six caves in Pang Mapha district. This includes 42 petrous bones and 22 tooth samples from individuals dated to 1,600-1,700 years cal. BP. A total of 33 complete mtDNA genomes were successfully sequenced and assigned haplogroups. A total 11 haplogroups could be categorized into three groups including, 1) a Southeast Asian specific haplogroup, i.e. F1f, F1a1a and B5a1d; 2) the basal M haplogroup which is prevalent in many Austroasiatic speaking groups, i.e. M1a3, M24b, M69 and M74; and 3) other haplogroups prevalent in areas outside Southeast Asia, e.g. N8 (south China), G2b1, D4 and D5a2a1b1 (China/Northeast Asia). Based on the haplogroup frequency, the ancient northern Thai population exhibited maternal relatedness to ancient samples from Nepal and Tibet and some present day Austroasiatic and Sino-Tibetan speaking groups. We conclude that the maternal genetic history of the Iron Age samples from northern Thailand are heterogenous, indicating a demic diffusion in the late prehistory. The result can be used as a comparative reference data with the earlier published data from China and Mainland Southeast Asia, and broadens our understanding of a western migration route into and/or through northwestern Thailand.