Application of autonomous navigation system permitted to unveil characteristic of deep and inaccessible portions of the sea widening the frontiers of near bottom geophysical investigation. A large improvement in resolution of near seafloor survey has been provided by coupling AUVs with standard marine geophysical sensors such as multibeam, high resolution seismic profiler, side scan sonar, ADCP/CTD and magnetometers. The high performance navigation capabilities of the last generation AUV able to flight at few meters above seabed, improved the accuracy in seabed mapping also providing details about its smallest features. Autonomous vehicles adoption proved to be very useful in case of magnetic investigation since the resolution of these data is strongly dependent by flight altitude. Scope of this work is to present preliminary results of S3MAG research project aimed to develop innovative AUV system equipped by a full magnetic tensor, very suitable for high precision magnetic investigation. Its low magnetic noise and the extremely easy-handling suggests to adopt the S3MAG AUV for multipurpose applications spanning from large spectrum geophysics research to more specific military/industrial needs.