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Why do executive agencies form coalitions? Legislative and parliamentarian coalitions are widely theorized and studied, but less attention has been paid to how and why agencies in the executive branch form coalitions. In contrast to legislator decisions to form voting blocs and parties, executive agencies are not fully autonomous agents engaged in divide-the-dollar type games, rather they are embedded in a separation of powers system that grants elected politicians authority over them. Executive agencies' dependence on the political branches calls for a distinctive theory of executive coalition building. This paper presents such a theory, arguing that agencies form coalitions to optimize their autonomy given their position in a separation of powers system. I then test the theory empirically with data on dozens of agencies over seventeen years, finding that agencies form coalitions when doing so optimizes their autonomy given their subservient position in the American separation of powers system.