Two highly active mud volcanoes located in 990–1,265 m water depths were mapped on the northern Egyptian continental slope during the BIONIL expedition of R/V Meteor in October 2006. High-resolution swath bathymetry and backscatter imagery were acquired with an autonomous underwater vehicle (AUV)-mounted multibeam echosounder, operating at a frequency of 200 kHz. Data allowed for the construction of ~1 m pixel bathymetry and backscatter maps. The newly produced maps provide details of the seabed morphology and texture, and insights into the formation of the two mud volcanoes. They also contain key indicators on the distribution of seepage and its tectonic control. The acquisition of high-resolution seafloor bathymetry and acoustic imagery maps with an AUV-mounted multibeam echosounder fills the gap in spatial scale between conventional multibeam data collected from a surface vessel and in situ video observations made from a manned submersible or a remotely operating vehicle.