South African debates on decolonization tend to centre on the injustices of the apartheid system rather than on those that occurred during the preceding centuries of colonialism. The violent conquest and forced assimilation of the Khoisan goes particularly unmentioned. Their absence in these debates is increasingly challenged by growing numbers of people claiming Khoisan identities and campaigning for indigenous rights in the post-apartheid era. By thinking through the socio-political and academic settings in which this absence is both manifested and contested, I distil issues that deserve further attention in order for the Khoisan to be meaningfully included in debates on decolonization. I scrutinize two main factors that add to the complexities of this 'layered' decolonization: the strategic essentialism surrounding Khoisan identity and culture, and the prevalent notion of an insurmountable incommensurability between indigenous people and others.