Günter Theißen (born 16 January 1962 in Mönchengladbach) is a German geneticist.
From 1992–2001, he was a group leader at the Max Planck Institute for Plant Breeding Research in Cologne.
In 2002, he was appointed to hold the chair of genetics at the University of Jena.
In his research, Theißen deals, among other things, with molecular genetics and evolution of plant development.
In particular, he and his group investigate special transcription factors encoded by MADS-box genes.