The article analyses how population genetics has impacted on nationalist discourses across the Taiwan Straits and affected the relationship between Taiwan and China since the 1990s. In Taiwan this cutting-edge science has helped to construct a native-based and Taiwan-centred national identity through promoting indigenous peoples’ rights, rejecting a blood-based, cross-Straits nationalism, and founding a pan-Pacific indigenous peoples’ community through genetic links and cultural affinity. In China, after subverting the nationalist myth of Peking Man (a Homo erectus group believed to be the common ancestor of the Chinese) by analysing genetic data, the same group of Chinese genetic scientists have constructed another nationalist myth of a genetically homogenous nationhood. Such a discourse not only valorizes Chinese nationalism through claiming a DNA-based Chineseness across ethnic distinctions but also asserts genetic links between China and Taiwan, therefore providing a ‘scientific’ basis for China’s nationalism in the new century.