This article critiques the limitations of orthodox liberal peacebuilding models in the context of South Sudan, arguing that their failure to account for endogenous political logics has contributed to recurrent conflict. It proposes a novel theoretical framework centred on the concept of Hybrid Political Orders (HPO), synthesising insights from African political sociology, conflict studies, and critical peace research. The framework is developed to systematically analyse the co-constitution, negotiation, and contestation of authority between formal state institutions and informal, customary, and militarised networks. The article elucidates the framework's theoretical implications for understanding sovereignty and legitimacy in post-colonial African states and outlines its practical application for designing context-sensitive peace interventions, monitoring mechanisms, and local ownership strategies in South Sudan.