The Iron Age of highland Pang Mapha in northwestern Thailand is characterized by a unique mortuary practice known as Log Coffin culture. Archaeological surveys and excavations have identified over 40 natural caves and rock shelters where large coffins dating to 2300-1000 years ago and carved from individual teak trees were mounted on stilts. Numerous multidisciplinary studies involving bioarchaeology, geology, dendrochronology, chronometric dating, and stable isotopes have been carried out to investigate the cultural development and population history of the highland area, noting that distinct carvings at the head and foot ends of the coffins suggest kin relationships among sites. In this study, we present ancient DNA from 32 individuals from four Log Coffin sites to study and compare their genetic ancestry profiles and links with ancient and present-day groups from Thailand and the surrounding regions. In addition, we evaluate the genetic interconnectedness within and between Log Coffin-associated sites and integrate our findings into the local and regional archaeology of Southeast Asia.