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This paper presents the design and implementation of control architecture for the ISiMI6000 AUV (Autonomous Underwater Vehicle) which is developing by MOERI-KIOST. The ISiMI6000 AUV is a sea-trial AUV up to the 6,000m depth. The control architecture of the ISiMI6000 AUV is a hybrid architecture consisting of the mission layer, the behavior layer, the logical sensor layer, and the library layer. The mission layer is in charge of the high level control of the AUV using TML (Tiny Mission Language). The TML can represent any mission easily and freely because it provides most functionality supported by general programming language. The behavior layer decides the AUV action by deterministic behavior arbitration mechanism. The logical sensor layer manages input data from sensors, output data from actuators, and environment data for AUV control using shared data pool. The library layer contains many useful libraries for fundamental functions such as hardware interface, communication and real-time management. The real-time management module provides soft real-time characteristic using software timer without real-time operating system. The control architecture has been implemented in two single board computers and two microcontrollers using C language and its software structure is hierarchy and modular.