Unlike some lichens, Endocarpon species often lack a distinct lower cortex, though they may have a loosely arranged layer of rounded or angular cells.

[4] Endocarpon lichens reproduce through small, rounded fruiting bodies called perithecia, which are embedded within the thallus.

Inside, the spore-producing tissue (hymenium) reacts with iodine-based stains, turning reddish or bluish with iodine (I+) and blue with potassium iodide (K/I+).

The spores themselves are muriform, meaning they are divided into multiple compartments by internal walls (septa), and they can be colourless, yellowish-brown, or dark brown.

In addition to sexual reproduction, Endocarpon can also produce asexual spores (conidia) within specialised structures called pycnidia, which are also embedded in the thallus.