Beneath this cortex lies the medulla, a loosely structured layer around 150 μm thick, made of interwoven fungal filaments (hyphae).

These structures have a proper exciple, or outer layer, made of tightly packed fungal cells (paraplectenchymatous) and can be up to 80 μm wide.

The tissue layer just below the spore-producing area, the subhymenium, is poorly defined, colourless, and contains loosely arranged fungal filaments, with some photobiont (algal) cells penetrating from below.

These spores are colourless, have a slightly wrinkled surface (rugulose}), and range from roughly spherical (globose) to oval (ellipsoid), without internal divisions (non-septate).

No asexual reproductive structures (pycnidia) have been observed to occur in Nebularia, and chemical analysis has revealed no distinctive lichen substances.