stylistic:tone, linguistic:paraphrasing, information:highlighting
Internal structure

A lichen consists of a simple photosynthesizing organism, usually a green alga or cyanobacterium, surrounded by filaments of a fungus. Generally, most of a lichen's bulk is made of interwoven fungal filaments, but this is reversed in filamentous and gelatinous lichens. The fungus is called a mycobiont. The photosynthesizing organism is called a photobiont. Algal photobionts are called phycobionts. Cyanobacteria photobionts are called cyanobionts.

The part of a lichen that is not involved in reproduction, the "body" or "vegetative tissue" of a lichen, is called the thallus. The thallus form is very different from any form where the fungus or alga are growing separately. The thallus is made up of filaments of the fungus called hyphae. The filaments grow by branching then rejoining to create a mesh, which is called being " anastomosed ". The mesh of fungal filaments may be dense or loose.

Generally, the fungal mesh surrounds the algal or cyanobacterial cells, often enclosing them within complex fungal tissues that are unique to lichen associations. The thallus may or may not have a protective "skin" of densely packed fungal filaments, often containing a second fungal species, which is called a cortex. Fruticose lichens have one cortex layer wrapping around the "branches". Foliose lichens have an upper cortex on the top side of the "leaf", and a separate lower cortex on the bottom side. Crustose and squamulose lichens have only an upper cortex, with the "inside" of the lichen in direct contact with the surface they grow on (the substrate). Even if the edges peel up from the substrate and appear flat and leaf-like, they lack a lower cortex, unlike foliose lichens. Filamentous, byssoid, leprose, gelatinous, and other lichens do not have a cortex; in other words, they are ecorticate.

Fruticose, foliose, crustose, and squamulose lichens generally have up to three different types of tissue, differentiated by having different densities of fungal filaments. The top layer, where the lichen contacts the environment, is called a cortex. The cortex is made of densely tightly woven, packed, and glued together (agglutinated) fungal filaments. The dense packing makes the cortex act like a protective "skin", keeping other organisms out, and reducing the intensity of sunlight on the layers below. The cortex layer can be up to several hundred micrometers (μm) in thickness (less than a millimeter). The cortex may be further topped by an epicortex of secretions, not cells, 0.6–1 μm thick in some lichens. This secretion layer may or may not have pores.

Below the cortex layer is a layer called the photobiontic layer or symbiont layer. The symbiont layer has less densely packed fungal filaments, with the photosynthetic partner embedded in them. The less dense packing allows air circulation during photosynthesis, similar to the anatomy of a leaf. Each cell or group of cells of the photobiont is usually individually wrapped by hyphae, and in some cases penetrated by a haustorium. In crustose and foliose lichens, algae in the photobiontic layer are diffuse among the fungal filaments, decreasing in gradation into the layer below. In fruticose lichens, the photobiontic layer is sharply distinct from the layer below.

The layer beneath the symbiont layer is called the medulla. The medulla is less densely packed with fungal filaments than the layers above. In foliose lichens, as in Peltigera, there is usually another densely packed layer of fungal filaments called the lower cortex. Root-like fungal structures called rhizines (usually) grow from the lower cortex to attach or anchor the lichen to the substrate. Fruticose lichens have a single cortex wrapping all the way around the "stems" and "branches". The medulla is the lowest layer, and may form a cottony white inner core for the branchlike thallus, or it may be hollow. Crustose and squamulose lichens lack a lower cortex, and the medulla is in direct contact with the substrate that the lichen grows on.

In crustose areolate lichens, the edges of the areolas peel up from the substrate and appear leafy. In squamulose lichens the part of the lichen thallus that is not attached to the substrate may also appear leafy. But these leafy parts lack a lower cortex, which distinguishes crustose and squamulose lichens from foliose lichens. Conversely, foliose lichens may appear flattened against the substrate like a crustose lichen, but most of the leaf-like lobes can be lifted up from the substrate because it is separated from it by a tightly packed lower cortex.

Gelatinous, byssoid, and leprose lichens lack a cortex (are ecorticate), and generally have only undifferentiated tissue, similar to only having a symbiont layer.

In lichens that include both green algal and cyanobacterial symbionts, the cyanobacteria may be held on the upper or lower surface in small pustules called cephalodia.

Pruinia is a whitish coating on top of an upper surface. An epinecral layer is "a layer of horny dead fungal hyphae with indistinct lumina in or near the cortex above the algal layer".

In August 2016, it was reported that some macrolichens have more than one species of fungus in their tissues.