Fishes were the first vertebrates. They are the only group of vertebrates that is almost exclusively aquatic, which was the primitive condition of all life.

All vertebrates are chordates and have evolved from invertebrate ancestors that resembled modern lancelets. Lancelets have a cartilaginous rod along the back (a notochord) in association with the main nerve cord and gill slits. All vertebrates have these features, although in most adult vertebrates the notochord is replaced by a backbone of vertebrae and may possess the gill slits only during the embryonic stage. Lancelets do not have jaws. An animal of the Cambrian period known as Pikaia closely resembled a lancelet.

The earliest known fishes lived during the Cambrian period. One example is Myllokunmingia, found from fossil deposits in China. Conodont animals also appeared in the Cambrian period and were probably also classifiable as fishes. Neither they nor the fishes of the early Ordovician period had jaws. Two classes of modern agnathan (jawless) fishes survive: lampreys and hagfishes, which today live by sucking blood from larger fishes.

One lineage of fishes evolved jaws during the Ordovician period. This allowed a major evolutionary advancement in the efficiency of predation. Many of the earliest jawed fishes, including the placoderms, were covered with bony armor, as the predatory arms race became severe. Placoderms apparently became extinct without descendants. Other lineages of jawed fishes survived to become the Chondrichthyes (cartilaginous fishes) and the Osteichthyes (bony fishes).

Cartilaginous fishes include the sharks and rays. Their skeletons consist only of cartilage. Teeth are not bones; shark teeth are structurally similar to their scales and are often the only part of the shark to be preserved as fossils. Many kinds of sharks diversified throughout the Paleozoic era. Today, some of them have very specialized features, such as the ability to navigate by electrolocation.

Bony fishes evolved in freshwater conditions and were restricted to freshwater for the first 160 million years of their existence. Scientists speculate that their bones were more important as a way of storing calcium, a mineral that could be scarce in freshwater, than as a skeletal reinforcement.

Bony fishes diverged into two major lineages:

- the ray-finned fishes, which have fins reinforced with bony rays that do not correspond to the fingers or toes of other vertebrates. The major lineage of ray-finned fishes is the teleosts, which includes most modern fish species.

- the flesh-finned fishes. These fishes diverged into two lineages: the lungfishes and the crossopterygians. Some lungfishes survive today in shallow tropical ponds. When the ponds have water, the oxygen levels are low and the lungfishes gulp air. When the ponds dry up, the lungfishes continue to breathe while estivating in the mud. The crossopterygian fishes have bones at the bases of their fins that correspond to the one upper and two lower limb bones of tetrapods (four-legged animals). Two branches of crossopterygian fishes became the coelacanths and the tetrapods.

Coelacanths were thought to have been extinct since the Cretaceous extinction 65 million years ago. However, in 1938, Captain Hendrick Goosen of the trawler Nerine brought a fish that had been caught deep in the Indian Ocean to Marjorie Courtenay-Latimer, curator of a museum in East London, South Africa. She identified the fish, now named Latimeria chalumnae, as a crossopterygian. Subsequent searches revealed that native fishermen of the Comoros Islands (in the Indian Ocean off the coast of Africa) reported that they had caught these fish for years and had thrown them back as inedible. In 1998 another species, Latimeria menadoensis, was found 10,000 kilometers away, in Indonesia, by a scientist on his honeymoon. . .

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