The Hanging Coffin represents a distinctive mortuary tradition practiced across southern China, Southeast Asia (e.g., the Log Coffin), and the Pacific approximately 3,000 years. Historical records attribute this funerary practice to the Bo people, a group that largely disappeared from documented history by the end of the Ming Dynasty (1,368-1,644 AD). Here we report eleven ancient genomes from four Hanging Coffin sites in China, alongside thirty whole genomes from the extant Bo people in Southwest China. We also sequence four ancient genomes from Log Coffin sites in northwestern Thailand. Our findings indicate that present-day Bo people derive a substantial proportion of their ancestry from practitioners of the Hanging Coffin mortuary tradition. Both ancient and modern groups exhibit elevated genetic affinity with coastal Neolithic populations from southern East Asia, who are ancestral to Tai-Kadai and Austronesian speakers. Unexpectedly, we also find evidence of long-range interactions and cultural inclusivity between Northeast Asian and Yellow River farmers and Hanging Coffin communities over 1,200 years ago. Finally, shared genetic components between Hanging (Log) Coffin populations in China and Thailand point to a common origin and a broader genetic and cultural network underlying this distinctive mortuary tradition across southern China and Southeast Asia.