| Johannes Musaeus | |
| Birth Date: | 7 February 1613 |
| Birth Place: | Langewiesen, Schwarzburg-Sondershausen |
| Death Date: | 4 May 1681 |
| Death Place: | Jena, Saxe-Jena |
| Nationality: | German |
| Fields: | Theologian and natural philosopher |
| Workplaces: | University of Jena |
| Alma Mater: | University of Erfurt |
| Doctoral Advisor: | Georg Grosshain |
| Doctoral Students: | Johann Georg Macasius |
| Footnotes: | He was the brother of Peter Musaeus. |
Johannes Musaeus (7 February 1613 – 4 May 1681) was a German Protestant theologian.
After visiting the Latin school in Arnstadt he studied at the University of Erfurt starting from 1633 in the Arts Faculty and in Jena with Damiel Stahl. In 1634 he received the Magister Artium, studying theology under Georg Grosshain, producing a thesis entitled: Disputatio Apologetica In qua Germanica B. Lutheri versio adversus Georgium Holzaium Jesuitam Ingolstad. defenditur In causa De Cultu Divino Enoschi. In 1643 he became professor of history and poetry. He obtained a doctorate to 1646 in theology and changed to the Theological Faculty.
He fought against the catholic controversial theologians V. Erbermann, J. Kedde, and Jacobus Masenius, and positioned himself against Socinianism. He was founder of the Jenenser Richtung followed by orthodox Lutherans.