A knowledge of fish anatomy is essential in identifying specimens. The head of a fish carries a number of structures. The eyes are without eyelids although sharks have a protective membrane, the nictitating membrane, which acts as an eyelid. Eye size varies with age within a species but can also be a distinguishing characteristic between species. There are nostrils, for detecting odours, on the snout, that part of the head before the eyes. Nostrils are blind sacs and do not connect with the mouth cavity. Their position and shape may be useful characters. Barbels are slender, fleshy structures on the snout or chin used for touch and taste. Their presence, number, position and length are important characters. Sharks and sturgeons have a small opening near the eye called the spiracle, not found in the bony fishes. Teeth may be found variously on the tongue, roof and floor of the mouth and even in the throat. The pharyngeal teeth of Cyprinidae are often useful characters in identification and may be dissected out from the posterior part of the gill cavity under the operculum using dissecting equipment. This requires some practice to avoid damaging the specimen too extensively. Some teeth are sharp and pointed for piercing and holding prey, while others are rounded and heavy for crushing food items covered by a protective shell. The side of the head behind the eye is the gill cover in bony fishes, composed mainly of one bone, the opercle, which protects the gills. The gill cover opens posteriorly; bony fishes have one opening on each side of the head, but lampreys have seven rounded openings and sharks five to seven vertical slits. The cheek is the area between the gill cover and the eye. Spines and scales may be found at various places on the gill cover and cheek. A membrane is found below the gill cover, supported by thin slivers of bone, the branchiostegals, and connected with the gill cover on the other side of the head. Under the gill cover lie the gills which serve in gaseous exchange. Gill rakers on the front of each gill arch serve to prevent food from damaging the gills and direct food into the gut. Rakers may be short and widely spaced where food items are large and easily deflected, or long and close together where food items are minute like plankton.

The head leads directly to the body; there is no neck. The body is made up mostly of a trunk. The caudal peduncle or tail stem starts behind the anal fin and ends at the tail fin. The number and presence of different types of fins on the body varies with the species of fish and is often a useful character for identification. The back may carry 1-3 dorsal fins and an adipose fin between the last dorsal fin and the tail fin. The tail (or caudal) fin is at the end of the body and may be forked, square cut, rounded, pointed, lanceolate or lunate. Its skeletal structure may be almost symmetrical or upturned at the end. This upturn is obvious in sharks and sturgeons which also have a large upper lobe to the tail fin and a smaller lower lobe. The anal fin, or fins, lies on the underside of the body surface behind the vent which is the exit for the intestine, kidney ducts and gonads. The pectoral fins are found behind the gill cover on each side of the body and a pair of pelvic fins are behind (abdominal), below (thoracic), or in front (jugular) of the pectorals on the lower body surface. An axillary pelvic scale above the pelvic fin streamlines the fin when it is pressed against the body. The pectoral fin may also have an axillary scale. All the fins except the fleshy adipose fin are supported by rays. Soft rays are flexible and jointed while spines are rigid, pointed and unjointed. The number of soft rays and spines in the various fins is very useful for identification.

Most fishes have a body covering of scales which may extend onto the head and certain fins. Notable exceptions are the catfish families Bagridae, Siluridae, Sisoridae and Heteropneustidae, which are completely naked. Rounded, smooth scales are called cycloid and are found in less advanced bony fishes. Large cycloid scales may easily detach, as in herrings (Clupeidae) but small cycloid scales can be embedded and hard to see as in the eel (Anguillidae). Ctenoid scales bear small teeth on the posterior margin and feel rough to the touch. Such scales are found in the more advanced bony fishes such as Percidae. Sturgeons have heavy bony plates called scutes. Sharks have placoid scales which can be so rough as to scrape the skin off a human. The teeth of sharks are modified placoid scales. Scales grow with the fish, laying down rings of material as do trees. In areas with a change of seasons, the growth rings are widely spaced during the summer growing season and cramped together in winter when growth is slow. Fish age can be determined from these rings. The energy expended in spawning is reflected in the scales which may resorb the edge producing a spawning check. A fish which lives and grows slowly in fresh water and then migrates to the rich feeding grounds of the sea will have this history reflected in the spacing of the growth rings. Scales can be "read" to reveal much about the life history of an individual fish. The scales also bear radii, or radiating lines, and their distribution can be useful in identification along with other scale characters such as shape and focus (growth origin) position. The scales are covered by an almost undetectable layer of skin. The skin contains mucus cells which give the fish a slippery feel and colour cells which give the fish its colour. Some fish are characteristically more slimy than others, e.g. the eel. Most fish have a distinctive colour pattern but this can change with age, maturity, behaviour, background, between sexes, and after death.

Fishes have a sensory lateral line system which runs along the flank and a similar system on the head. The extent and development of these systems varies with the species of fish. The lateral line is a tube in the skin with openings to the outside through pores in the scales. A lateral line pore count is often used in separating fish species.

The internal structure of a fish may be summarised as follows. The gills and teeth have already been mentioned. After these structures, the mouth cavity narrows to an oesophagus which passes to a straight, U- or J-shaped stomach. Pyloric caeca, which produce enzymes, may be attached at the junction of the stomach and intestine in some fishes and counts of these caeca are used in identification of some species. The intestine ends at the vent. The length of the intestine varies with the diet. Fishes which feed on plant material have long guts while those that feed on animals have a short, often s-shaped intestine. Fish have a liver, a reddish organ at the front of the body cavity. The liver may be very large in sharks and form a significant part of the body weight. There may be a small, green gall-bladder associated with the liver. The swimbladder (gasbladder) is a gas-filled sac with thin walls lying near the top of the body cavity where it functions as a buoyancy organ and can be used to transmit sounds to the brain or even produce sounds by means of special drumming muscles. The swimbladder shape has been used to characterize species. Some fishes have a poorly developed swimbladder or none at all, since they live on the bottom of stream beds and must avoid being swept away. Just below the backbone above the swimbladder are two long, dark-coloured kidneys and below these are the ovaries, which may be filled with eggs, or the testes which produce the sperm. A small urinary bladder lies at the end of the body cavity. The body cavity is lined with a membrane which may vary in colour from silvery-white to jet black. The main body muscles are in the form of W-shaped, interlocking blocks and this arrangement helps produce the sinuous body movements by which fish swim.

Lampreys (Petromyzontidae) differ in structure from bony fishes. They lack true jaws and have a round, suctorial mouth armed with teeth. There is a single nostril on top of the head rather than a pair on each side. There are no scales or paired fins (pectorals and pelvics). There are seven rounded gill openings in a row behind each eye. The larval lamprey is called an ammocoete and lives buried in fine sediments, filter feeding minute particles from the water. In this stage it lacks teeth and the eye is poorly developed.

Sharks also have a somewhat different structure from bony fishes. Some species produce living young rather than eggs, while in others the embryo is laid in a horny egg-case known as a mermaid's purse when it washes up on a beach. Male sharks have claspers derived from the pelvic fins, which serve to ensure that sperm are delivered to the female. The length of time food stays in the gut of sharks, and also sturgeons, is increased by a spiral valve. The food follows the spiral around rather than going straight through the gut and so there is more time for digestion and absorption. There is no swimbladder in sharks, which have to swim constantly to stay above the bottom. Sharks produce teeth in multiple rows, and as older teeth at the front of the jaw fall out, new ones move forward to replace them.

The skeleton includes the skull comprising the cranium, which contains the brain, the jaws, gill arches, operculum and other associated bones. The cranium also contains small objects known as otoliths in the inner ear. These aid in sensing change of direction and in balance. Otoliths can be characteristic of species. There is a vertebral column with ribs anteriorly enclosing and protecting the body cavity and its contents. The number of vertebrae is a useful character and can be counted easily, without damage to the fish, by taking x-rays. A tail skeleton supports the tail fin and the pectoral and pelvic girdles support their respective fins. There are fin supports too for the dorsal and anal fins. Lampreys, sharks and sturgeons have a skeleton composed of cartilage, a substance not as strong as bone, but when impregnated with salts (like shark teeth) are remarkably effective.

Most characters used for fish identification are external for convenience. The most used internal characters are gill raker counts, pharyngeal teeth counts, gut shape and body cavity lining colour, pyloric caeca counts and vertebral counts.

The general structure and biology of fishes is covered in various general works. Coad (1993; 1995b) gives a list of general ichthyology texts and the Dictionary of Ichthyology describes various anatomical terms.

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