Because of their soft bodies, hydrozoans have a meager fossil record, especially before the Cenozoic (65 million years ago). Among the few ancient fossils are jellyfish-like hydrozoans (chondrophores) that today are represented by little “by-the-wind sailors.” These hydrozoans float around the sea, sometimes in large groups, using a gas-filled structure (the pneumatophore). Because the pneumatophore is made partly of hard chitin, it has the potential to fossilize. Fossil pneumatophores have been found from Precambrian deposits (more than 550 million years old). Beginning in the Cenozoic, some hydrozoans developed hard body parts that fossilized well. For example, colonial forms with calcium carbonate exoskeletons included fire corals (Millepora sp.) and lace corals (Sylaster sp.). While fragile, their skeletons accumulated into large reefs that preserved under the right conditions. Many hydroids have skeletons made of chitin that only occasionally preserve.

Fossils of soft-bodied Cnidarians are rare, although they may be some of the earliest fossils of complex animals. Paleontologists have debated whether fossils from the Ediacaran (more than 540 million years ago) that look like jellyfish and sea pens are Cnidarians. The first definite Cnidarian fossils are from the Cambrian (about 500 million years ago). Some Cnidarians begin to make mineralized skeletons then, which were more likely to fossilize than the soft body parts underneath. During the Paleozoic, Cnidarians underwent a diversification into many forms. Jellyfish, hydrozoans, and corals emerged as distinct lineages. While various extinction events impacted Cnidarians along the way, these lineages survived to the present day. Colonial corals, whose skeletons accumulate into large reefs, ended up leaving a substantial fossil record. Because corals are sensitive to environmental variables, such as temperature and water quality, they have been used as indicators of past climate and other conditions.