In Europe bat rabies in Daubenton's bats (Myotisdaubentonii) and in Pond bats (Myotis dasycneme) caused by the European bat lyssavirus 2 (EBLV-2) has been confirmed in less than 20 cases to date. Here we report the second encounter of this virus species in Germany. A Daubenton's bat found grounded in the zoological garden in Magdeburg died shortly after. In the frame of a retrospective study the bat carcass was eventually transferred to the national reference laboratory for rabies at the Friedrich-Loeffler-Institute for rabies diagnosis. Lyssavirus was isolated and characterized as EBLV-2.