East Asia is widely concerned as one of the important places for the dispersal and evolution of the Anatomically Modern Human (AMH). How the diverse ethnic groups in East Asia originated and diversified is also widely focused by different disciplines of Anthropology. The adoption of genetic data had provided new clues for reconstructing the genetic history of East Asian populations. Genetic studies supported the hypothesis that the AMHs originated from Africa’s Homo sapiens at about 200 kilo years ago (kya) and then migrated out of Africa at ~100 kya, followed by expansions into the whole East Asia since their arrival in Southern East Asia at 5~6 kya along the coastal route. Early Homo Sapiens might have genetic contribution to the non-African AMHs. Early settlement, cultural assimilation, population migration and genetic exchanges are crucial in the origination and evolution of East Asia populations. Previous studies made detailed analysis for the genetic history of East Asian populations, which largely resolved the longstanding divergence between archaeology and history. However, this needs further verification by whole-genome sequencing and ancient DNA studies. Here we briefly reviewed the progresses of genetic studies in exploring the population origin, dispersal and diversification in East Asia, which improved understanding of the evolution of East Asian populations. We also prospected the future of genetic studies in revealing the prehistory of East Asians.