Fish Anatomy: Interactive 3D Model of a Bony Fish

A bony fish has three body regions: the head (up to the rear edge of the gill cover), the trunk (which holds the body cavity), and the tail (behind the anus). It breathes with four pairs of gills under a bony operculum, floats with a gas-filled swim bladder, swims with W-shaped blocks of muscle, and steers with median fins (dorsal, caudal, anal) and paired fins (pectoral and pelvic). Its heart pumps blood in a single loop: heart → gills → body → heart.

The yellow perch is the fish most often dissected in school. It is a spiny-rayed teleost: its fins have true spines, its pelvic fins sit under the pectoral fins, and it has rough ctenoid scales. More than 96% of living fish species are teleosts, so what you learn on a perch applies to most fishes.

Anterior = towards the snout; posterior = towards the tail; dorsal = the back; ventral = the belly; lateral = the side. Median fins lie on the midline; paired fins come in left and right pairs. A fin formula lists spines in Roman numerals and soft rays in Arabic numerals: the perch anal fin is II, 6–8.

These labeled diagrams of a yellow perch match the 3D model. Use them as a fish anatomy worksheet: print the unlabeled version and label the fish anatomy yourself, or colour it in.

Worksheet and colouring versions: unlabeled fish outline (label the fish / colouring page).

The external anatomy of a fish includes the mouth, nostrils, eyes, operculum, lateral line, scales, vent and fins. The head ends at the free edge of the operculum. The lateral line is a row of pored scales that senses water movement. Perch scales are ctenoid (with tiny teeth on the rear edge) and record the fish's age as yearly rings.

• Mouth (terminal): Takes in food and the water used for breathing. The perch's protrusible upper jaw shoots forward as the mouth opens, sucking prey in.
• Nostrils (nares): Water flows in through the front opening, over the olfactory rosette, and out of the back one. They are for smell only.
• Eye: Vision in colour and dim light. Each eye sees a wide field to its own side.
• Operculum (gill cover): Protects the gills and works as a pump: as the mouth closes, the opercula swing out and then close, keeping water flowing one way over the gills.
• Lateral line: Senses water movement and low-frequency vibration. Fish use it to school, find prey, avoid obstacles and detect predators in the dark.
• Scales (ctenoid): Flexible armour that protects the body while still letting it bend.
• Caudal peduncle: Transfers the force of the trunk muscles to the tail fin.
• Anus (vent): Releases faeces.
• Urogenital pore: Releases urine from the urinary bladder and, in the breeding season, eggs or milt.

A perch has eight fins: two dorsal fins, a caudal fin and an anal fin on the midline, and paired pectoral and pelvic fins. Each fin is a thin membrane stretched over spines (stiff, unsegmented) and soft rays (flexible, segmented lepidotrichia), anchored inside the body by pterygiophores or girdle bones.

Fin counts: Scott & Crossman (1973).

A fish's face is built from the snout, the jaws, the nostrils, the eyes, the cheek and the gill cover. The perch mouth is terminal; its upper jaw (premaxilla) slides forward when the mouth opens. Each side of the snout has two nostrils that lead to a blind smell pit, not to the throat. The gill cover is made of four bones (opercle, preopercle, subopercle, interopercle); the perch opercle ends in a flat spine, and the preopercle is saw-edged.

• Snout: Carries the nostrils and leads the body through the water.
• Premaxilla: Bites and grips prey. In perch it slides forward (protrudes) as the mouth opens.
• Maxilla: Swings forward when the mouth opens and pushes the premaxilla out.
• Lower jaw (dentary): Closes against the upper jaw to grip prey.
• Cheek: Covers the jaw-closing muscle (adductor mandibulae).
• Opercle: Forms most of the gill cover and ends in a flat spine in perch.
• Preopercle: Supports the gill cover and carries part of the head lateral line canal.
• Branchiostegal rays: Spread and fold the membrane during breathing, enlarging the gill chamber.
• Isthmus: Joins the head to the body on the underside and holds the hyoid and heart region.

The internal anatomy of a fish is packed into the body cavity behind the heart. In a perch opened from the left side you see, from front to back: the liver, the gonad (ovary or testes), the stomach with three pyloric caeca, the looping intestine, the dark spleen, and above everything the silvery swim bladder. The dark red kidney lies above the swim bladder, pressed against the backbone.

• Liver: Makes bile, stores fat and glycogen, processes nutrients from the gut, and makes yolk proteins for eggs.
• Gall bladder: Stores bile and releases it into the intestine to emulsify fats.
• Stomach: Stores prey and starts digestion with acid and the enzyme pepsin.
• Pyloric caeca: Increase the surface area for digestion and absorption of nutrients; they secrete digestive enzymes.
• Intestine: Digests food and absorbs nutrients and water.
• Pancreas (diffuse): Makes digestive enzymes and the hormones insulin and glucagon.
• Spleen: Makes and stores blood cells, removes old red blood cells and helps fight infection.
• Swim bladder (physoclistous): Controls buoyancy, so the fish can hover at any depth without swimming. Gas is added by the gas gland and removed at the oval.
• Kidney (trunk kidney): Filters blood and makes urine. In fresh water it produces large amounts of dilute urine to get rid of the water that soaks in through the gills.
• Urinary bladder: Stores urine and reabsorbs some salts before urine is released.

Swim bladder types. Perch, bass and most spiny-rayed fishes are physoclistous: the swim bladder is closed. A gas gland fed by a counter-current rete mirabile adds gas, and the oval removes it. Carp, koi, salmon and trout are physostomous: a pneumatic duct joins the swim bladder to the gut, so they can gulp or burp air.

Fish gills are four pairs of bony gill arches, each carrying two rows of red gill filaments on its outer side and stiff gill rakers on its inner side. Each filament is lined with microscopic plates (secondary lamellae) where blood flows opposite to the water. This counter-current flow keeps blood next to water that has more oxygen than it does, all along the lamella.

• Gill arches: Support the gill filaments and carry the branchial arteries.
• Gill filaments: Gas exchange. Each filament carries rows of microscopic plates (secondary lamellae) where blood takes up oxygen and releases carbon dioxide.
• Gill rakers: Strain food and keep food and debris away from the delicate filaments.
• Pseudobranch: Receives already oxygenated blood and sends it to the eye's choroid gland. It is not used for breathing.
• Afferent branchial arteries: Deliver deoxygenated blood to the gill filaments.
• Efferent branchial arteries: Collect oxygen-rich blood from the gills.

A fish heart has one atrium and one ventricle, so it is called two-chambered, but blood passes through four parts in a row: sinus venosus → atrium → ventricle → bulbus arteriosus. It lies in the pericardial cavity under the throat, just behind the gills. It pumps only deoxygenated blood, forward through the ventral aorta to the gills; oxygenated blood then flows to the body in the dorsal aorta. This is a single circulation, unlike the double circulation of mammals and birds.

• Sinus venosus: Receives blood from the cardinal veins (via the ducts of Cuvier) and hepatic veins and passes it to the atrium. It contains the pacemaker.
• Atrium: Fills the ventricle.
• Ventricle: Pumps blood forward through the bulbus arteriosus to the gills.
• Bulbus arteriosus: Smooths the pulse: it stretches as the ventricle beats and recoils between beats, protecting the fragile gills from pressure spikes.
• Ventral aorta: Distributes blood to the four pairs of afferent branchial arteries.
• Dorsal aorta: Supplies oxygenated blood to the muscles and organs.
• Cardinal veins: Return deoxygenated blood to the heart.

The fish brain is small and lies in a row inside the skull. From front to back: olfactory bulbs (smell), telencephalon (cerebrum: learning and memory), the large paired optic lobes (vision), the cerebellum (coordination) and the medulla oblongata (breathing, heart rate, hearing and lateral line), which continues as the spinal cord. In a sight-hunter like the perch, the optic lobes are the largest part.

• Olfactory bulbs: Process smell information from the olfactory rosettes in the nares.
• Telencephalon (cerebrum): Learning, memory and spatial behaviour, plus some smell processing.
• Optic lobes (optic tectum): Process vision and combine it with lateral-line and other senses to aim the fish at prey.
• Cerebellum: Coordinates swimming, balance and posture.
• Medulla oblongata: Controls breathing movements and heart rate, and receives input from the inner ear, lateral line and taste buds.
• Hypothalamus and pituitary: Controls hormones for growth, reproduction, stress and salt balance.
• Spinal cord: Carries signals between brain and body and runs swimming reflexes.

A fish eye has a flat cornea and a hard, perfectly round lens that bulges through the pupil. Under water the cornea barely bends light, so the spherical lens does the focusing. A fish focuses by moving the lens backwards and forwards with the retractor lentis muscle, instead of changing its shape as we do. Fish have no eyelids.

• Cornea: Lets light in and protects the eye.
• Iris: Frames the pupil. In most teleosts, unlike in sharks, the pupil can change size little or not at all.
• Lens (spherical): Focuses light on the retina. Fish focus by moving the lens forwards and backwards with the retractor lentis muscle, not by changing its shape.
• Retina: Rods detect dim light; cones detect colour. The signals leave through the optic nerve.
• Choroid gland (choroid rete): A counter-current net of blood vessels (rete mirabile) that raises oxygen pressure behind the retina, feeding its high oxygen demand.
• Optic nerves: Carry visual information.

A bony fish skeleton has a skull (neurocranium) with jaws and gill-cover bones, a vertebral column of 38–41 hourglass-shaped vertebrae in perch, ribs around the body cavity, and fin supports. The pectoral girdle (cleithrum) is joined to the back of the skull, so fish have no neck. The tail fin is carried by the fan-shaped hypural plate. The small "pin bones" in a fillet are intermuscular bones in the muscle sheets.

• Skull (neurocranium): Protects the brain and sense organs and anchors the jaws, gill arches and pectoral girdle.
• Abdominal vertebrae: Support the trunk and protect the spinal cord; their ribs surround the body cavity.
• Caudal vertebrae: Form a flexible column for the side-to-side tail beat.
• Neural spines: Protect the spinal cord and anchor the epaxial muscles.
• Haemal spines: Protect the caudal artery and vein that run through the haemal arches, and anchor muscle.
• Ribs (pleural ribs): Support the body wall around the abdominal organs.
• Intermuscular bones (pin bones): Stiffen the myosepta and help transmit muscle force.
• Pectoral girdle (cleithrum): Supports the pectoral fins and forms the back wall of the gill chamber and front of the heart cavity.
• Pelvic girdle: Anchors the pelvic fins.
• Pterygiophores: Support the fin rays and give attachment to the small muscles that raise, lower and tilt them.
• Hypural plate: Supports the caudal fin rays.

Most of a fish's body is swimming muscle, arranged in myomeres: W-shaped blocks separated by thin myosepta. A horizontal septum divides the epaxial (upper) from the hypaxial (lower) muscle. Most of it is white muscle for bursts of speed; a thin strip of red muscle along the side powers steady cruising.

Female yellow perch have a single ovary, unusual among fishes: it begins as a pair and fuses early in development. In spring it is huge and orange, full of eggs that are laid as a gelatinous, accordion-folded ribbon. Males have a pair of smooth, white testes. Both release their eggs or sperm through a pore behind the anus, and fertilisation happens in the water. Use the Female/Male switch on the model to compare.

• Ovary: Produces eggs. Before spawning it can fill much of the body cavity.
• Oviduct (gonoduct): Carries eggs out of the body at spawning.
• Testes: Produce sperm (milt).
• Sperm ducts: Release sperm during spawning. Fertilisation is external, in the water.
• Urogenital pore: Releases urine from the urinary bladder and, in the breeding season, eggs or milt.

Fish do have a tongue, but it is a stiff pad over the basihyal bone on the floor of the mouth. It has taste buds but no muscles of its own, so it cannot move like a human tongue. In trout and bonytongues it even carries teeth.

Cartilaginous fish (sharks, rays and chimaeras) differ from bony fish in several key ways: a skeleton of cartilage, 5–7 separate gill slits with no operculum, no swim bladder (a large oily liver gives buoyancy), tooth-like placoid scales, a heterocercal tail, a spiral valve in the intestine, and claspers on males for internal fertilisation. Compare them on the shark anatomy page.

The perch is a good template, but fish anatomy varies a lot. These species often come up in class:

Bass anatomy

Largemouth and smallmouth bass are sunfishes (Centrarchidae), close in body plan to perch: a spiny and a soft dorsal fin, thoracic pelvic fins, ctenoid scales and a closed swim bladder. Their two dorsal fins are joined by a deep notch rather than separate, and the largemouth's upper jaw reaches past the back of the eye.

Koi fish anatomy

Koi are ornamental common carp. They have no teeth in the jaws but grind food with pharyngeal teeth in the throat, two pairs of barbels on the upper jaw, and no true stomach. Their swim bladder has two chambers and stays open to the gut (physostomous). Small bones of the Weberian apparatus link the swim bladder to the inner ear, giving carp and their relatives (the Otophysi) excellent hearing. Perch have no Weberian apparatus.

Salmon anatomy

Salmon and trout have a small, rayless adipose fin between the dorsal fin and the tail; it may help sense or control flow over the tail. Their pelvic fins are abdominal (far back), their scales are smooth (cycloid), their swim bladder is physostomous, and they have dozens of pyloric caeca. Most salmon are anadromous: their kidneys and gills switch between saltwater and freshwater salt balance as they migrate.

Puffer fish anatomy

Pufferfish inflate by pumping water (or air) into a very stretchy stomach; they have no ribs or pelvic fins to stop the body swelling. Their four teeth are fused into a beak (Tetraodontidae means "four teeth"). Many species carry tetrodotoxin, a nerve poison concentrated in the liver, ovaries and skin.

Angler fish anatomy

In anglerfishes the first dorsal-fin spine has moved onto the snout as a fishing rod (illicium) tipped with a lure (esca); in deep-sea species the esca glows with symbiotic bacteria. In some deep-sea anglers tiny males fuse permanently to a female and share her blood supply, a form of sexual parasitism linked to changes in their immune system.

Barreleye fish anatomy

The barreleye (Macropinna microstoma) has green-lensed, tubular eyes inside a transparent, fluid-filled shield over its head. The eyes can rotate from looking straight up to looking forward when it feeds. The two dark spots above its mouth that look like eyes are actually its nostrils.

Lionfish anatomy

Lionfish are scorpionfishes with long, separated fin spines that carry venom: 13 dorsal spines, 3 anal spines and one in each pelvic fin. Their fan-like pectoral fins are used to herd prey.

Betta fish

Bettas share the perch body plan but have long, flowing fins, an upturned mouth and a labyrinth organ above the gills for breathing air. See betta fish anatomy.

Note: jellyfish and starfish are not fish at all; they are invertebrates (a cnidarian and an echinoderm). See jellyfish anatomy and starfish anatomy.

Test yourself, then click to check each answer.

1. Which fin pushes a fish forward?

   The caudal (tail) fin.

2. What covers and protects the gills of a bony fish?

   The operculum (gill cover).

3. How many pairs of gill arches does a perch have?

   Four.

4. Name the four parts of the fish heart in the order blood flows.

   Sinus venosus, atrium, ventricle, bulbus arteriosus.

5. Which organ lets a perch hover without swimming?

   The swim bladder.

6. What does the lateral line detect?

   Water movement and vibration.

7. Where is the fish kidney?

   Along the underside of the vertebral column, above the swim bladder.

8. What are the finger-like pouches at the end of the stomach called?

   Pyloric caeca.

9. Spines or soft rays: which are segmented?

   Soft rays (lepidotrichia).

10. Which part of the brain is largest in a perch?

    The optic lobes (optic tectum).

Doing a lab? Follow the step-by-step perch dissection guide with lab questions and an answer key.