Scytonema usually forms wooly mats or clumps as part of the metaphyton and periphyton of swamps, bogs, and temporary pools. The filaments are sometimes free-floating or creeping along the substrate. Most species are aerial or subaerial on wet rocks, wood, or soil, or are found in lake periphyton or along sea coasts. Over 100 species have been described, many from tropical habitats.

Scytonema and certain other cyanobacteria genera can be especially abundant in alkaline wetlands where they often become encrusted with calcium carbonate. Assemblages of Scytonema, Aphanothece, Chroococcus, Leptolyngbya, Lyngbya, Microcoleus, Phormidium, and Schizothrix have been found

in alkaline systems in the Caribbean, Cuba, the Florida Everglades, and coastal Belize and Mexico.

 

Scytonema is the algal phycobiont associated with several orders of lichens. Some species are associated with the lichens forming the cryptogamic crusts in deserts and grasslands that increase soil fertility and guard against erosion.

Scytonema ocellatum and some Tolypothrix species produce tolytoxin, a powerful antifungal antibiotic that is only slightly toxic to humans.

Scytonema and some other cyanobacteria produce a yellow-brown pigment in their mucilage called scytonemin. Scytonemin protects the cyanobacteria in Antarctic ponds and other extreme environments from high levels of solar radiation and the resulting DNA damage.