Houttuyn was born in Hoorn, studied medicine in Leiden and moved to Amsterdam in 1753.

He published many books on natural history, e.g. Natuurlyke Historie of uitvoerige Beschryving der Dieren, Planten en Mineraalen, volgens het Samenstel van den Heer Linnaeus, in 37 volumes (1761-1773), following Carl Linnaeus' division into the animal kingdom, the plant kingdom, and the mineral kingdom.

His areas of interest encompassed Pteridophytes, Bryophytes and Spermatophytes.

He is commemorated by the genus Houttuynia, a member of the Saururaceae from China and Japan.

Martinus Houttuyn was the co-writer of the volumes 2, 3, 4 and 5 of Nederlandsche Vogelen.