St. John's Church is located in the Seebach district of Mühlhausen and is named after St. John the Evangelist. The Romanesque-style church was first mentioned in a document in 1123. The church was rebuilt in the early Gothic style between 1250 and 1260. The towering half-timbered spire dates from the 18th century. The baroque altar wall was designed around 1701 by an unknown master with stone reliefs, motif panels and oil paintings from the 16th and 17th centuries. They depict members of the Berlepsch family and the founder of the ornithological station. The chimes consist of three bells. The organ is by Wilhelm Rühlmann.

The church is Protestant and is under the care of the Mühlhausen church district. Church services are held here regularly.