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.

He fought against the catholic controversial theologians V. Erbermann, J. Kedde, and Jacobus Masenius, and positioned himself against Socinianism.