AbstractObjectivesWe aim to detect demographic history and early farming‐related migration of the crossroad area in the junction of east Asia (EA) and southeast Asia (SEA).Materials and methodsWe collected and genotyped 87 individuals from 6 Tibeto‐Burman and Austroasiatic‐speaking populations including Bai, Pumi, Hani, Lahu, Wa, and Blang with nearly 700,000 genome‐wide SNPs. We subsequently analyzed genetic structure and admixture using our merged dataset including both ancient and modern eastern Eurasians with PCA, ADMIXTURE, Refine‐IBD, f statistics and qpAdm.ResultsWe observed population substructure within the studied Tibeto‐Burman populations. The northern Tibeto‐Burman groups (Bai and Pumi) had a predominant genomic legacy associated to millet‐farming from North China and also high frequencies of Y‐chromosomal haplogroup O2a2b1‐M134 (xM117) and its sub‐clades. By contrast, southern Tibeto‐Burman groups (Lahu and Hani) had more than 60% genomic legacy associated to rice‐farming, which is prevalent in present‐day Tai‐Kadai, Austronesian and Austroasiatic speaking populations. We observed strong genetic affinities between Austroasiatic populations in Yunnan (Blang and Wa) and mainland southeast Asia.DiscussionOur study revealed that both demic migrations and cultural interactions from north to south and east to west since the Late Neolithic have shaped the genetic structure of populations at the crossroads of EA and SEA. The dominant genomic legacy associated with millet‐farming in northern Tibeto‐Burman populations indicates large‐scale Neolithic migrations from the Upper‐Middle Yellow River Basin. The rice‐farming expansion has deeply influenced the genetic profile of both southern Tibeto‐Burman and Austroasiatic populations, suggesting migrations from east to west via both inland and coastal routes.