Fish Dissection

Yellow perch, Perca flavescens

Image: Yellow perch (public domain).

In this lab you'll have a chance to dissect preserved specimens of three species of fish.

The species for today's lab are:

  • Freshwater Drum, also called Sheephead (Aplodinotus grunniens) (EOL)
  • Freshwater Perch (Perca flavescens). (EOL, Wikipedia, ADW)
  • Gray Perch, also called Longspine Grunt (Pomadasys macracanthus). A marine fish. (EOL)

A pre-dissected perch

We have this dissected specimen, embedded in plastic, in lab.

Perch dissected 2019 11 12 15.32.33

I can't tell what all the numbers are supposed to be pointing at, but here's my best guess:

  1. Mouth
  2. Eye
  3. Seems to be pointing at part of the operculum, which has been cut away. The operculum is the bony covering over the outside of the gills.
  4. Gill. The gill is supported by a series of bony arches, with a large blood vessel in each arch. These vessels are visible in pink at the top of the arch. The gill lamellae in this specimen are dark, and contain capillaries.
  5. I'm not sure what this is pointing at.
  6. Heart.
  7. Liver. The liver is partly cut away, revealing part of the digestive tract.
  8. Part of the kidney, which has been pulled down in the dissected specimen. The kidney in a living fish looks like a long, flat strip of blood-filled tissue just ventral to the vertebral column.
  9. Swim bladder. This swim bladder is large and divided into two sections. At the narrow point between the two sections, on the ventral side, you can see a spongy -looking blob of tissue with blood vessels. This is the gas gland, which fills the swim bladder with oxygen by acidifying the blood and forcing oxygen to be released from the hemoblobin.
  10. Dorsal fin
  11. I think this is pointing at the bony rays extending upward from the vertebrae.
  12. Vertebral column
  13. Caudal (tail) fin
  14. ?
  15. Anal fin
  16. Vent (the single opening for urine, gametes, and feces)
  17. Gonad
  18. Part of the digestive tract.

External anatomy

Teeth: Fish have teeth, which come in a wide range of sizes and shapes. In addition to the teeth in the jaws, many species of fish also have additional pharyngeal teeth in the throat.

Pectoral fins: A pair of fins on the sides of the fish just behind the gills, corresponding to the pectoral girdle and forelimbs of tetrapods.

Pelvic fins: A pair of fins on the ventral part of the fish, corresponding to the pelvic girdle & hind limbs of tetrapods.

Dorsal, caudal (tail), and anal fins: These are the unpaired fins along the midline of the body.

Lateral line: You should see a pigmented stripe marking the location of the lateral line sense organs, which contain hair cells for detecting water movement. Can you see any evidence of the lateral line canals or organs?

Vent: Fish have a single opening for the urinary, genital, and digestive tracts; this opening is called the vent. Everything posterior to the vent is the tail, which is quite long. You could safely cut off your fish's tail while leaving the internal organs intact for later dissection.

Nares (nostrils): used for olfaction, not for breathing; they open into a small chamber that contains olfactory epithelium. Unlike in humans, the nostrils do not connect to the mouth.

Operculum: The hard cover over the gills. During ventilation, water is taken into the mouth and pushed out through the opening beneath the operculum.


Before you begin your dissection, take a look at the perch skeleton:

Perch skeleton, with pectoral and pelvic fins labeled.

In a later lab, you'll be able to compare this to the skeletons of other vertebrates.

There are two sets of paired fins: the pectoral fins, which are homologous to your arms, and the pelvic fins, which are homologous to your legs. The other fins (dorsal, anal, and caudal or tail) aren't in left/right pairs.

Examining the skeleton, you can see where the coelom would be: in the space enclosed by the ribs. All the ribs are anterior to the anal fin. On a whole fish, you'll see that the vent is just in front of the anal fin. This gives you a good idea where to start your dissection.


Gill arch with gill rakers and filamentsUsing scissors, cut away the operculum to expose the gills. Each gill is supported by a bony gill arch, with the spiny gill rakers projecting forward. The gill rakers protect the gills and prevent prey items from escaping through the gill area when the fish is trying to swallow them. Note the filaments of the gills, each with many lamellae. You will be able to see this better under the dissecting microscope.

The fish’s blood must flow through the gills to get oxygenated, so the gills are filled with blood vessels. The heart is located just behind the gills, but you won’t be able to see it until you cut the body open. You’ll come back to the heart in a little while.

(Image from ClipArt Etc.)

References: gills

Respiratory System FNM

Fish Dissection - Gills exposed and Dissection of a Bluespotted Flathead - Gills from the Australian Museum.


 Inside the body cavity

Look at the Fish Necropsy Manual before you start; you'll find some good dissection images there.

Open up the main coelomic cavity by making an incision from the vent forward to just behind the head. Note that you cut through several layers of tissue: skin, muscle, and the peritoneum, a smooth membrane lining the inside of the body cavity. You may want to remove one side of the body wall, exposing the internal organs.


The liver is large; it secretes bile into the gall bladder, from which the bile passes into the intestine. The gall bladder usually looks like a small green blister on the surface of the liver.

Digestive tract

The digestive tract of fish is roughly similar to that of mammals. Food passes from the mouth down the esophagus to the stomach. You may be able to see pyloric ceca, which function as accessory digestive glands (mammals don’t have these). Look closely at the stomach. The pyloris, where partially digested chyme exits the stomach, is not at the posterior end; it's closer to the anterior. You'll see small blood vessels at the posterior end of the stomach, but that's not where the chyme goes. Look for the pyloric ceca to find the beginning of the intestine. The intestine is fairly long. You may find remnants of food in the stomach. This is likely to smell bad; I recommend cutting the stomach after you're done with everything else. You may also be able to find the pancreas near the pyloric ceca.

Digestive System on the Fish Necropsy Manual

Swim bladder

The swim bladder is a large light-colored structure near the dorsal side of the body cavity. It is easy to find if it is filled with gas, but easy to miss if it is empty. Bony fish can adjust their buoyancy by putting gas into the swim bladder. The most abundant gas in the swim bladder is oxygen, which is released from the blood in the gas gland. The gas gland generates lactic acid, acidifying the blood in the gas gland and causing it to release its oxygen (remember the Bohr shift? In the gas gland, oxygen is released mainly by a related effect, the Root effect.). This gland is accompanied by a specialized countercurrent to maintain the incredibly strong gradient of oxygen partial pressure between the swim bladder and the blood. Some fish can have over 100 atmospheres of oxygen partial pressure in the swim bladder, but their blood can never contain more O2 pressure than the surrounding water, which never contains more O2 pressure than the air (0.2 atm).

Since the swim bladder develops from the esophagus, it is covered under the Digestive System on the Fish Necropsy Manual.


In a fish that is ready to reproduce, the gonads can be the largest organs in the body cavity; otherwise these organs can be quite small. If your fish is a female, you should be able to see the small eggs in the single ovary; in a male, the two testes will appear smooth and milky.

Kidneys & urinary bladder

Fish kidneys don't create a strong osmotic gradient, which is why fish can't make hyperosmotic urine. The kidneys of fish do not look at all like mammalian kidneys.  They are long and thin and dark, and located along the very top of the body cavity, just ventral to the vertebral column. Most of the nitrogenous waste is secreted by the gills, not the kidney. Urine produced by the kidney enters the urinary bladder, which exits into the vent. See the Fish Necropsy Manual for good photos.

In addition to its osmoregulatory functions, the kidney also performs hematopoiesis, the production of new blood cells. This might seem like a surprising function for a kidney, but the kidneys of mammals also secrete a hormone (erythropoietin, or EPO) that regulates hematopoiesis.

Hematopoietic System on the Fish Necropsy Manual


The heart is located just beneath the gills; the heart's entire output goes to the gills first, after which the oxygenated blood is sent to the rest of the body. After you've examined the other organs, try to cut away more of the surrounding tissues to reveal the heart. At first it may look like a dark blob, but feel it with your fingers. The firm, rubbery part is the ventricle, which pumps blood. The softer part is the atrium, which collects blood under lower pressure prior to pumping. Blood from the ventricle is pumped directly into the gills. Remember that in fish, the blood is pumped just once as it makes its way through the gills and systemic circulation. The fish heart is considered to be two-chambered, but you may observe more chambers than that; see this article for a description. For more detail and an excellent illustration, see Cardiac morphology and blood pressure in the adult zebrafish.

Circulatory system on the Fish Necropsy Manual

Brain & Eyes

It's possible, but difficult, to examine the brain in these fish. The best strategy is to cut off the head near the first vertebra. Then carefully remove the bony top of the head, revealing the top of the brain.

If you dissect the eyes, you'll find the lens inside. Fish lenses are nearly spherical; unlike mammals, fish focus their eyes by moving the lens back and forth rather than changing the shape of the lens. The lens, made of protein, is transparent when the fish is alive, but becomes white and almost opaque after the fish dies.

Nervous System on the Fish Necropsy Manual

How old is your fish?

Two methods are widely used to determine the age of fish: examination of scales and examination of otoliths. Both these structures tend to form annual rings, so you may be able to determine the age of your fish by counting rings. Both these approaches often require some specialized equipment, but it's worth a try to see if you can do it using the tools in our lab.


Pull a scale off your fish, clean it up and examine it on a dissecting microscope, with the light coming from below. Perch have a scale type called ctenoid scales. The scales are composed of a combination of protein (largely collagen) and calcium minerals.

Can you see rings on the scales? Can you count them? Do different scales from the same fish tell you the same age?

If you are dissecting a beltfish, this approach won't work; beltfish don't have scales.


 Otoliths are bones in the inner ear. They play key roles in helping an animal detect acceleration and determine which way is up. These small bones also grow in annual rings, which correspond to the age of the fish. In larger fish, the otoliths are so thick and opaque that the rings are not visible. These large otoliths must be sliced into thin sections with a special saw to see the rings. However, the otoliths of smaller fish may allow you to see the rings without sectioning the otolith. Can you see any sign of rings on the otoliths of our fish in lab?

References: Determining the age of fish

Estimating the age of fish (Wikipedia). This article describes different methods, including the use of scales and otoliths.

Fish scales tell a story. Delaware Division of Fish & Wildlife. A brief summary of the rationale for aging fish.

Introduction to Aging Fish: What Are Otoliths? Florida Fish and Wildlife Conservation Commision.

Fish Age Determination. NOAA Fisheries Service. NOAA also has an Age Reading Demonstration page to show how age is determined from otoliths.

 Yellow Perch Otolith Removal. A short video on YouTube showing how to find and remove the otoliths.


You should be prepared to identify any of the structures labeled on the diagrams on this page or listed in bold type in the text of this page.

  • Gonads: ovary or testes
  • Gills
  • Heart. You should be aware that there are two chambers: an atrium and a ventricle.
  • Intestine
  • Kidney
  • Liver
  • Peritoneum and mesenteries
  • Pyloric ceca
  • Stomach
  • Swim bladder (also called gas bladder or air bladder)

References & further reading

Fish Anatomy from Wikipedia. Not a great article, but it may be the best one available.

Fish Necropsy Manual. An excellent source for dissection information.

Dissection of Organs from the Adult Zebrafish. Tripti Gupta, Mary C. Mullins. JOVE (Journal of Visualized Experiments). This article provides a detailed video on dissecting zebrafish, a species commonly used for laboratory studies in developmental biology. Zebrafish are tiny compared to the fish you'll see in lab, but the anatomy is very similar. There is also a pdf version of this article.

Dissection of a Blue Mackerel and Dissection of a Bluespotted Flathead from the Australian Museum.

Drum fish dissections. Photos of dissected fish from CSULB. Other images here.

Perch Dissection from Udo Savalli's Bio 370 at ASU.

Salmonids in the Classroom. Salmon dissection from Fisheries and Oceans Canada.

Striped Bass illustration from Jared Travnicek, scientific illustrator.


In Bio 6A, sometimes we dissect fresh fish from the grocery store. Our preferred species is called Beltfish, but it also goes by several other names, such as Largehead hairtail.

Online videos

Bony Fish (Perch) Anatomy from McGill University. Dissection of a perch.

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