A prothallus, or prothallium, (from Latin pro = forwards and Greek θαλλος (thallos) = twig) is usually the gametophyte stage in the life of a fern or other pteridophyte. Occasionally the term is also used to describe the young gametophyte of a liverwort or peat moss as well. In lichens it refers to the region of the thallus that is free of algae.

The prothallus develops from a germinating spore. It is a short-lived and inconspicuous heart-shaped structure typically 2–5 millimeters wide, with a number of rhizoids (root-like hairs) growing underneath, and the sex organs: archegonium (female) and antheridium (male). Appearance varies quite a lot between species. Some are green and conduct photosynthesis while others are colorless and nourish themselves underground as saprotrophs.