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Parallels between rebel governance and theories of state building is an important concern for current policy approaches on engagement with rebel groups and for achieving stable political settlements. Rebel groups develop ideologies, create internal leadership structures, and form civilian support constituencies over time in a bid to create ‘proto-states’ in territories under their control. These characteristics signal rebel commitment to state building that is a necessary precondition for their transition into effective and legitimate governments. Whilst the weakness of the state is clearly a contributing factor in a rebel group’s involvement in governance, recent research increasingly shows that instances of rebel governance can have an autonomous dynamic as well. In this paper, I argue that armed group agendas relating to governance present variations between what can be termed, proto-state and anti-state forms. Anti-state governance, i.e., when an armed group that stands in violent opposition to the state, engages in governance, has different implications for legitimacy, compared with proto-state governance. In the latter case, an armed group seeks to replace the regime in power and pursues an alternative political agenda towards that end. Proto-state groups tend to provide widely shared public goods often directly associated with legitimate institutions such as security and justice. They set up civilian administration with varying levels of civilian involvement motivated by larger political goals. Proto-state groups are likely to have well-developed political wings. They demonstrate willingness toward political participation, and towards acquiring political legitimacy. I test this argument in the case the cases of the Sudan People’s Liberation Army/Movement (SPLA/M) and the Moro Islamic Liberation Front.