The history of each group of fish being examined should be closely followed, particularly that information related to water source, pond, cage or system number, species, age, stocking rate, growth performance, survival rates, feeding activity, food conversion rate, grading history, parasite or pathogen burdens and treatment history. Any abnormalities in any of these areas should be noted when they are observed so that these data are available for future reference if required.

Water quality

Basic water quality parameters such as temperature and dissolved oxygen should be regularly monitored. Other variables such as salinity, and presence or absence of toxic phytoplankton and jellyfish should be recorded in fish in seacages, while on land and in recirculation systems monitoring of additional parameters such as ammonia, nitrite and nitrate, water hardness and pH should be implemented. Ideally these records should be available for the entire history of each group of fish being examined.

Gross examination

Detailed investigations should be restricted only to live or moribund fish. Dead fish are of limited usefulness unless they are very fresh. Each fish should be examined for ectoparasites, external lesions Figure 1 and abnormal behaviours, such as lethargic swimming Figure 2, flashing (rubbing its side on the tank or cage), increased opercular movements or other visible signs of stress. These signs should be noted on a data sheet prior to capturing and handling the fish. Once the fish has been captured it should be anaesthetised Figure 3 using an approved anaesthetic such as Aqui-S (see Recipes page) to make it easier to handle and allow more time to examine the skin and gills Figure 4 for monogenean and copepod ectoparasites. Measure and weigh the fish if required and enter this data on the data sheets supplied. Then examine the fish for deformities Figure 5, and check the eyes for cataract Figure 6, the latter of which can indicate nutritional disorders. Check the fins for erosion Figure 7, which may indicate infection by bacteria or protozoan parasites. Also note any reddened lesions or ulcers on the body or at the base of the fins which may also indicate infection by bacteria, protozoa or ectoparasites Figure 8. If any of the above are observed or suspected, scrapes of affected skin, gills and fins should be obtained on a glass slide and examined under a microscope to obtain a presumptive diagnosis.

Collection of blood

If blood is to be taken for analysis (usually easiest in fish over about 10 cm long), the anaesthetised fish should be inverted and blood collected from the caudal vein Figure 9 using an appropriate sized needle and syringe (see Recipes page). Collect up to 1 ml of blood and place it into a heparinised microtainer, invert 5 or 6 times, spin with a hand centrifuge and store at 4C until the bloods can be analysed, usually as soon as possible.

Dissection and internal examination

Larvae and very small fish (less than 1.5 cm) can be fixed in 10% seawater formalin whole. Fish between 1.5 and up to 4 cm long can be killed by anaesthetic overdose (Aqui-S, see Recipes page), then slit open the stomach ventrally to allow entry of the fixative before placing the whole fish into 10% formalin. For fish larger than around 5 cm long , they should be dissected as follows: After an external examination the fish can be placed back in the anaesthetic to die of overdose. Using double strength anaesthetic such as Aqui-S, this can take 5 to 10 minutes. Then the opercula should be cut off with a sharp pair of scissors Figure 10 and the gills examined for grossly visible lesions. Any areas with visible lesions should be promptly excised, placed in a histology cassette (Simport M493) and fixed in formalin for histopathology (see below). If no lesions are visible instead excise a standard section of the first gill arch Figure 11, see below). Excise and examine the remaining gill arches under a dissection microscope for lesions or ectoparasites. The gut cavity is then opened starting from the vent using either scissors or a scalpel, and the ventral belly flap is removed from one side of the fish to expose the internal organs with three cuts Figure 12. Examine each of the following organs for any abnormalities - liver, spleen, stomach, pyloric caecae, intestines, swimbladder and kidney. Take good quality digital photographs of any grossly visible lesions for later analysis.


Excise a standard section of gill Figure 11 and liver Figure 13. Then sever the oesophagus Figure 14 and remove the remainder of the guts and swimbladder to allow sampling of the kidney Figure 15 for routine analysis. Under special circumstances other tissues (eye and/or lens, brain, spleen, intestine, heart, head kidney, gonad) may also be included in histopathological analyses. These tissues should be excised, placed in histopathology cassettes (Simport M493) and fixed in either 10% neutral buffered formalin or 10% seawater seawater (see Recipes page). Ensure that the volume of fixative used is at least 5 times that of the tissues being fixed. If grossly visible abnormalities are observed in any of these organs, make sure the abnormal tissues are included in the samples excised for histopathology.


Excise the gall bladder (a transparent sac running off the liver containing green or yellow coloured bile) and place a small amount of bile on a microscope slide - put on a coverslip and examine the bile wet for myxosporean parasites. You can also examine all other organs using wet squash techniques if required. Smears can be examined wet (useful for detecting motile protozoa and bacteria) or air dried then processed using a differential stain kit (e.g. DiffQuick, see Recipes page). Open the stomach and intestines with a longitudinal incision and examine the mucosa for helminth parasites.

Bacteria and Virus testing

Bacteriology and virology testing use specialised techniques which should be conducted using methods recommended by the diagnostic laboratory which will undertake the sample screening. Contact DigsFish Services or the laboratory responsible for processing your samples for more information on their desired methods of sample collection.

Sending samples

Once all samples are processed replace allow the material in formalin to fix for 48-72 hours. Then follow the instructions in the transport page to forward the samples and data sheets to DigsFish Services (for clients in Australia). Any remains from the diseased fish examined can either be frozen at -20C for short term storage, then disposed of in landfill, and/or buried or incinerated - do not put them back into the water.