Hans-Joachim Merker (7 October 1929 – 18 August 2014) was a German physician and anatomist.
He was Professor of Anatomy at the Free University of Berlin from 1972 to 1998, and served as Dean of the Faculty of Medicine from 1980 to 1981.
He was noted for his research on the fine structure of connective tissue, the morphology of hormone effects, and embryological and embryotoxic problems, and his research was central in the development of medical research utilising electron microscopy.
Hans Georg Baumgarten noted on his death that he was "not only a chair-holder, but a philosopher, humanist, anthropologist, developmental biologist, transdisciplinary scholar and scientist".