In keeping with the Navy's policy to remove humans from harms way, the Autonomous Underwater Vehicle (AUV) is replacing human divers for many missions. The Advanced Marine Systems Lab at Florida Atlantic University (FAU) has developed a small, magnetically friendly, modular plastic AUV called Morpheus designed for coastal applications and especially suited for very shallow water (VSW) mine reconnaissance. Currently employed sensor technologies on AUVs have certain deficiencies and limitations when used across the wide gamut of naval targets and environments, and a strong requirement exists for a sensor or sensors to fill these niches. The Real-time Tracking Gradiometer (RTG) selected for this integration is truly such a niche sensor because its capabilities are not degraded by media interfaces or environmental conditions. It is an experimental prototype fluxgate magnetometer array developed by Quantum Magnetics for the Coastal Systems Station (CSS) and was designed to be man portable and self contained. While limited by physics in detection range, it is capable of detecting ferrous targets under the worst environmental conditions, even when the target is buried. While not having the range of sonar, the RTG does not respond to the false alarms that are indicated by sonar, and since it is capable of also providing range and bearing information, it provides an invaluable niche filling classification tool. The placing of any magnetic sensing system on a conventional AUV is a non-trivial problem. The standard AUV is designed around materials and components that were selected to maximize performance without regard to the magnetic properties of the materials used in its fabrication. To minimize the degradation of sensor performance caused by the platform, several steps must be taken. These include; the substitution of nonferrous components for ferrous, maximizing the separation between the sensor and magnetic field sources, minimizing current loops and using auxiliary current and field sensors capable of generating noise canceling signals. To maximize utility, the magnetic sensor systems should also provide range, bearing and magnetic target strength. While all data and results contained in this paper have been obtained with land-based testing, they are easily adapted to the underwater environment of the AUV. The RTG was recently attached to the Morpheus, and data collected with the unmodified Morpheus powered and undergoing simulated sea motion table. These tests indicate that integration, while not trivial, is indeed feasible, and work is continuing toward mounting the sensor internal to the AUV and implementing the required noise mitigation solutions.