This article seeks to understand the logic of ethnicisation that took place from the outset of the civil war in South Sudan and the resulting polarisation of identities, using the case of the Western Equatoria region as an example. From the beginning of the conflict, inhabitants of the region saw all their daily practices conditioned by their ethnicity. The text argues that such polarisation is the result of the formation of new competing identity regimes carried by both the government and the opposition groups involved in the conflict. It is the configuration of these identity regimes and their interaction that define ethnicisation dynamics, visible through practices of control, surveillance and violence, along with the individual and collective behaviours that they produce in return. This article provides an account of both the identity regimes established, through the categorisations at play and the hierarchical principles adopted, and the processes by which ethnicity has become a political affiliation and a criterion for reorganising social and political space.