New fiber optic oxygen microsensors (microoptrodes) for use in aquatic environments have recently been developed as an alternative to commonly used CLark-type oxygen microelectrodes. The microoptrodes have the advantage of no oxygen consumption and no stirring sensitivity combined with a simple manufacturing process of the sensors. To avoid problems inherent to luminescence intensity measurements like photobleaching, signal dependency on the optical properties of the surrounding medium and system drifts, a novel measuring system was developed. This system uses a phase modulation method to evaluate a signal phase shift that is caused by the oxygen dependent luminescence lifetime. The measuring system is based on simple solid state technology. High reliability and low costs of the system can therefore be combined with the ability of miniaturization and low power consumption. The system consists of three units: 1) the microoptrode with the optical setup [glass fiber coupler, optical filters, lenses, light source (light emitting diode) and light detection (photon multiplier tube)], 2) the analogue signal processing unit, including a special phase detection module, and 3) the digital signal processing unit, a personal computer or a microcontroller for control of the measuring system, display and data storage. First measurements of oxygen depth profiles in sediments and biofilms at high levels of ambient light demonstrated the advantages of phase shift based O2 measurements as compared to intensity based measurements with microoptrodes.