AUV photomosaics of the seafloor at the shallow-water Milos hydrothermal system. Photomosaics were acquired with the Sparus II (Iqua, Girona) AUV and constructed from vertically acquired still images. Images were acquired in July 2019 at the Paleochori and Spathi Bays. Photomosaics are provided as geotiffs (UTM Zone 35). This dataset includes both original photomosaics, that show distortions due to AUV navigation drift, and georeferenced photomosaics, that have been registered with the associated drone photomosaics at these same areas.