Security sector reform (SSR) is often presented as a pathway to building unified national forces, yet in practice it can entrench ethnically structured military power. The concept of ethnic militarisation by reform captures how processes intended to integrate armed actors instead reproduce patterns of patronage, factional command, and identity-based control. Moving beyond a descriptive case account, the manuscript examines SSR as a domain of ethnic politics in post-conflict South Sudan, situating these dynamics within broader debates on African political order, state formation, and institutional design. Focusing on South Sudan, with comparative reference to Rwanda and the Democratic Republic of the Congo, the study addresses three interrelated questions: how the composition of South Sudan’s unified armed forces, formally integrated through DDR and SSR processes, continues to reflect and reinforce patronage networks rather than consolidate a national institution; how Dinka, Nuer, and Equatorian identity logics shape promotion, command appointments, and resource allocation within the SSPDF, and how these dynamics intersect with intra-community factional loyalties; and under what conditions international SSR assistance inadvertently legitimises and sustains ethnically organised armed forces, as well as what design changes might alter these incentives. Methodologically, the study combines analysis of SSPDF officer rosters and promotion records, interviews with SSR practitioners (including UNMISS, EUTF, and bilateral advisors), process tracing of DDR implementation from 2006 to 2023, and structured comparison with Rwanda’s post-genocide military integration and the DRC’s FARDC integration challenges. The contribution lies not only in explaining South Sudanese and comparative