Autonomous underwater vehicles are vehicles that are entirely or partly independent of human decisions. In order to obtain operational independence, the vehicles have to be equipped with a specialized software. The main task of the software is to move the vehicle along a trajectory with collision avoidance. Moreover, the software has also to manage different devices installed on the vehicle board, e.g. to start and stop cameras, sonars etc. In addition to the software embedded on the vehicle board, the software responsible for managing the vehicle on the operator level is also necessary. Its task is to define mission of the vehicle, to start, stop the mission, to send emergency commands, to monitor vehicle parameters, and to control the vehicle in remotely operated mode.The paper presents architecture of the software designed for biomimetic autonomous underwater vehicle (BAUV) that is being constructed within the framework of the scientific project financed by Polish National Center of Research and Development.