Abstract: The Balloon Experimental Twin Telescope for Infrared Interferometry (BETTII) is an 8-meter interferometer which operates on a high-altitude balloon. BETTII had its first successful engineering flight in June 2017. In this paper we discuss the design of the control system for BETTII, which includes the coarse pointing loop and the estimator controls algorithm (Extended Kalman Filter) implemented in FPGA. We will also discuss the different system modes that we defined in the controls system loo…