The nature of human difference in Southeast Asia continues to excite scientific research and speculation, as it has for centuries. Only now scientists are more likely to describe humanity in the region in terms of population genetics than rigid racial typologies. They base their analyses on variations in nucleic acid arrays rather than skin colour, hair texture, morphology, blood groups, and languages. Their themes tend to diversity and shared connections, not the older absolutist styles of taxonomy, category, or breed. Their studies often are oriented toward the deep past, especially the prehistory of human origins and migrations, or toward contemporary biomedical opportunities, shifting away from research that might consolidate racial regimes useful in population management and state orders. Even so, nationalist talk of the 'Filipino genome' and the 'Indonesian genome' persists: recently a scientist has proposed, for example, that his 'genetic data resource will protect and empower the Filipino people'. 1 Generally, though, contemporary genetic research into human difference in Southeast Asia follows a dispersive logic, a complex patterning that no nation-state or region can contain, an intricate diffusion respecting no boundaries, not even Wallace's biogeographical line. It has become a project consistent with global imperatives. Thus the 'detailed palimpsest of Indonesian genetic diversity', according to recent investigators, 'is a direct outcome of the region's complex history of immigration, transitory migrants, and populations that have endured in situ since the region's first settlement'. 2 Scientists continue to tell us who we really are, or were, or even might bebut in new modes and with odd inflections. In this special issue of the Journal of Southeast Asian Studies (JSEAS), we bring together articles that outline a critical historyan elucidative archaeologyof a century and more of such research into human difference in Island Southeast Asia, revealing This special issue brings together papers originally presented at the panel 'Colonial and National Racializations in Southeast Asia' as part of the 7th EuroSEAS meeting in Lisbon, in July 2013.