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We present a navigation system for autonomous indoor flight of micro-scale Unmanned Aircraft Systems (UAS) which is based on a method for accurate monocular vision pose estimation. The method makes use of low cost artificial landmarks placed in the environment and allows for fully autonomous flight with all computation done on-board a UAS on COTS hardware. We provide a detailed description of all system components along with an accuracy evaluation and a time profiling result for the pose estimation method. Additionally, we show how the system is integrated with an existing micro-scale UAS and provide results of experimental autonomous flight tests. To our knowledge, this system is one of the first to allow for complete closed-loop control and goal-driven navigation of a micro-scale UAS in an indoor setting without requiring connection to any external entities.