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Recent scholarship has shown that authoritarian regimes originating in violent revolutions from below or counterrevolution from above are especially durable. A major reason is sustained military loyalty to the dictatorship. These civilian-dominated regimes are protected from both coups and from color revolutions. In this paper, we ask whether similar dynamics arise in regimes arising from violent rebellions, even when they do not assume the form of revolutions or counterrevolutions. We find that the durability of rebel regimes depends on organizational factors rather than the mere fact of large-scale violence. We argue and demonstrate that three key factors, unfolding at three successive historical junctures, shape whether political leadership will successfully control military commanders after victory: 1) whether a civilian front controls the creation of an armed wing before the war; 2) whether political leadership is located locally or is exiled during the war; and 3) whether political or military leadership presides over the transition from a guerrilla force to a conventional army after the war. Emerging rebel regimes can gain or lose control over their military commanders at any of these three key junctures. The civil-military relations that the new regime inherits from war profoundly shapes regime survival through coup vulnerability and military loyalty during mass protests.