The type specimen is the Solnhofen Specimen of Archaeopteryx (BSP 1999). Discovered in the 1960s near Eichstätt, Germany and described in 1988 by Wellnhofer (as a specimen of Archaeopteryx), it is currently located at the Bürgermeister-Müller-Museum in Solnhofen. It was originally classified as a Compsognathus by an amateur collector.
Although Elżanowski found significant differences between Wellnhoferia and Archaeopteryx, a 2007 study by Mayr et al.  found Wellnhoferia was a specimen of Archaeopteryx lithographica. Senter and Robins (2003), however, supported Elżanowski's naming of a new genus.