In this chapter a system for tracking the motion of box jellyfish Tripedalia cystophora in a special test setup is investigated. The goal is to measure the motor response of the animal given certain visual stimuli. The approach is based on tracking the special sensory structures - the rhopalia - of the box jellyfish from high-speed video sequences. The focus has been on a real-time system with simple building blocks in the system. However, using a combination of simple intensity based detection and model based tracking promising tracking results with up to 95% accuracy are achieved.