Bellubrunnus is known from a single complete articulated skeleton, the holotype of the genus, having the accession number BSP–1993–XVIII–2. It was found in the summer of 2002 by an excavation team led by Monika Rothgaenger, the namesake of the species. It was prepared in 2003 by Martin Kapitzke and at first identified as an exemplar of Rhamphorhynchus. It is preserved in ventral view, meaning that the underside of the skeleton can be seen on the limestone slab. The specimen is currently housed in the Bürgermeister-Müller-Museum, although it is cataloged for, and a possession of, the Bayerische Staatssammlung für Paläontologie und historische Geologie. It comes from a quarry at Kohlstatt near the village of Brunn, Upper Palatinate, in a layer of rock that underlies the better-known Solnhofe