The Monterey Bay Aquarium Research Institute (MBARI) has developed an autonomous seafloor mapping capability for high resolution mapping of the deep ocean seafloor. The D. Allan B. is a 0.53 m diameter, Dorado class autonomous underwater vehicle equipped with a 200 kHz multibeam sonar, 110 kHz and 410 kHz sidescan sonars, and a 2-16 kHz subbottom profiler. All components of the vehicle are rated to 6,000 m depth. Using precise navigation and attitude data from a laser-ring-gyro-based inertial navigation system integrated with a Doppler velocity log sonar, the D. Allan B. can image the deep-ocean seafloor and shallow subsurface structure with much greater resolution than is possible with sonars operated from surface vessels. Typical survey operations use a vehicle speed of 1.5 m per second (3 knots) and an altitude of 40 m to 100 m. The D. Allan B. has now been operated in a variety of settings, including submarine canyons (Monterey Canyon, Barkley Canyon), submarine fan systems (Redondo Channel, Lucia Chica, San Clemente), seamounts (Axial Seamount), methane hydrate outcrops and gas seeps (Santa Monica Basin, Barkley Canyon), and cable route surveys across continental margin slopes (Monterey Bay). The bathymetry surveys achieve a vertical precision of 0.1 m; surveys from a 50 m altitude achieve 1 m lateral resolution and surveys from up to 100 m altitudes achieve lateral resolutions less than 2 m. The subbottom profile data provides resolution of ~0.1 m with penetrations up to 50 m in soft sediments. These survey data are sufficient in quality and resolution to use in conjunction with visual observations and sampling for mapping benthic habitats in the deep ocean.