Apothecia and other similar structures on the lichen are the places where the fungus reproduces itself. In this cross-section you can see the spores are produced in little sacs that are surrounded by a protective cup-like body.
Apothecia, Perithecia, and Mazedia are all reproductive structures. Each one produces spores which disperse and can produce a new fungus, but each of these structures looks and functions differently. Perithecia and Mazaedia are discussed on other pages.
Apothecia are different than the parts of the lichen that distribute both the fungus and the algae together. To find out about them check out soredia and isidia.
Orange apothecia on a crustose lichenReddish apothecia on a foliose lichen

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