A number of internal and external parasites are of importance in aquaculture.
The disease called "Ich" or "white spot disease" has been a problem to aquarists for generations. Fish infected with this organism typically develop small blister-like raised lesions along the body wall and/or fins.
Tavares-Dias, Lemos and Martins 2010 report that 64% of ornamental fish collected from the middle Negro River, State of Amazonas were parasitized by at least one parasite species. The authors found infection as follows: Monogenea 36.7%, Ichthyophthirius multifiliis (Ciliophora) 20.6%, Trichodina spp. (Ciliophora) 4.0%, Piscinoodinium pillulare (Dinoflagellida) 1.3%, Tetrahymena sp. (Ciliophora) 0.89%, and Procamallanus sp. (Nematoda) 0.4%.
Chilodonella and Tetrahymena
Dopheide et al. 2011 assessed the feeding preferences of the free-swimming filter feeder Tetrahymena sp. and the surface-associated predator Chilodonella sp. Both protozoans feed on bacteria such as Pseudomonas costantinii and Serratia plymuthica, found on bacterial biofilms, and exert an important impact on the morphology of such biofilms.
Climate change increases incidence of some parasitic diseases 
Global warming may increase the incidence of parasitic diseases. Karvonen et al. 2010 presented a long-term multi-pathogen data sets on the occurrence of pathogenic bacterial and parasitic infections in relation to increasing temperatures in aquatic systems.
The authors found that the prevalence of infections increased with temperature. Diseases caused by Ichthyophthirius multifiliis and Flavobacterium columnare increase with elevation of temperature of the water. However, Karvonen and colleagues caution that the biology of each disease and local conditions must be considered, because the incidence of some diseases respond inversely to a temperature increase, such as noted with diseases caused by Ichthyobodo necator, and some do not respond to temperature variations, such is the case of Chilodonella spp.
Piscinoodinium pillulare and Tricodina
Nile tilapia from Brazilian fish farms were found by Jerônimo et al. 2011 to be infested by Piscinoodinium pillulare (Dinoflagellida), which was the most dominant parasite followed by Trichodina magna e T. compacta (Ciliophora), Cichlydogyrus sclerosus, C halli, C. thurstonae, Scutogyrus longicornis (Monogenoidea), copepodids Lernaeidae gen. sp. The authors reported higher infestations by protozoan during autumn and winter and higher infestations by metazoan in spring and summer.
Ambiphyra Apiosoma and Epistylis
Ambiphyra and Apiosoma are a sessile ciliates that can be found on the skin, gills, and fins of fish. Both are not particularly pathogenic if present in low numbers, but in high numbers, these parasites can cause significant damage. Overpopulation and poor sanitation, high organic loads and deterioration of water quality are frequently associated with heavy infestations.
Apiosoma piscicola (Blanchard 1885) was reported from fry of Carassius auratus (Var. pengze) and Ctenopharyngodon idella during parasite surveys in May 2005 and June 2006 at Hongze Lake, China. Its synonyms, Glossatella cylindriformis (Chen 1955) and Apiosoma magna (Banina 1968), were clarified by Li et al 2011 in their study.
Wu et al 2011 describe the morphology of the oligohalobic peritrichous ciliate, Epistylis chlorelligerum Shen, 1980. Zooids of Epistylis. chlorelligerum are characterized by green-colored endoplasm containing symbiotic algae.
Ferguson et al. 2011 studies the impacts of parasites on Oregon coastal coho salmon (Oncorhynchus kistuch), identifying 21 different species of parasites, such as Nanophyetus salmincola, Myxobolus insidiosus, Apophallus sp., Sanguinicola sp., Trichodina truttae, Epistylis sp., Capriniana piscium, an unidentified metacercariae in gills, Myxobolus sp. in brain, Myxidium salvelini and Chloromyxum majori in kidney, Pseudocapillaria salvelini and adult digenean spp. in the intestine.
Hexamita is a small intestinal Flagellate parasite commonly found in the intestinal tract of freshwater fish. Hexamita sp.with morphological characteristics similar to Hexamita meleagridis was identified in stunted diarrhoeic 1- 12- week old native turkey poults by Dezfoulian et al.2010.
Two Ichthyobodo species are known to infect Atlantic salmon (Salmo salar L.). Ichthyobodo necator sensu stricto (s.s.) is a freshwater parasite, and Ichthyobodo sp. II sensu Todal et al. (2004), found in both fresh- and seawater.
Isaksenet al. 2011 found that Ichthyobodo sp. II present a unique SSU rDNA sequences and different morphology, compared with Ichthyobodo necator ss. The authors concluded that Ichthyobodo sp. II. represents a novel species and propose the name Ichthyobodo salmonis sp. n.
Guo and Woo 2009 describe important fish parasites causing disease outbreaks in fish farms and transmission of diseases between farmed and wild fish. The authors highlight the importance of four
economically important fish parasites: Cryptobia salmositica (haemoflagellate), Loma salmonae (microsporidian), Gyrodactylus salaries (monogenean), Lepeophtheirus salmonis (copepod), and Caligus rogercresseyi (copepod).
The Myxozoa are a group of parasitic animals of aquatic environments. Many have a two-host lifecycle, involving a fish and an annelid worm or bryozoan.
The most significant diseases worldwide caused by myxosporeas in cultured fishes are PKD-Proliferative Kidney Disease, caused by a Malacosporea member,Tetracapsuloides bryosalmonae, and whirling disease, caused by a Myxosporea member Myxobolus cerebralis; both diseases affect salmonids. Furthermore, Enteromyxosis is caused by Enteromyxum leei in cultured marine sparids, while "Hamburger disease” or Proliferative Gill Disease is caused by Henneguya ictaluri in catfish and Sphaerosphora renicola infections occur in common carp.
All microspoidia are intracellular parasites that require host tissue for reproduction. They invade vertebrates and invertebrates. such as insects, crustaceans, fish and humans.
The microsporidia have recently been recognized as a group of pathogens that have potential for waterborne transmission. Of primary concern are the microsporidian species that infect the human gastrointestinal tract, Enterocytozoon bieneusi and Encephalitozoon syn. Septata intestinalis. they present a special challenge to the water treatment industry with regard to detection and filtration. Wolk et al. 1999 presented a spore counting and cell culture model for microsporidia.
Coccidia are intracellular parasites found in wild-caught and cultured fish. They are potential pathogens. According to Bangoura 2011 the pathogenic coccidia species Eimeria bovis and Eimeria zuernii are widespread in German dairy and fattening facilities. Eimeria oocysts were found positive in 95.4% of samples. Eimeria bovis was found in 76.9% of samples and Eimeria. Zuerniib in 83.1%. The number of oocysts excreted depended on the floor type, the age of the calves and the time after rehousing. Eimeria zuernii had a greater influence on the occurrence of diarrhoea than Eimeria bovis. The authors concluded that control measures to reduce coccidia incidence should be improved in Germany.
Detection of coccidian parasites
Honma, Suyama and Nakai 2011 investigated the coccidian parasites in cranes using faecal DNA using polymerase chain reaction-based capillary electrophoresis (PCR-CE), employing genetic markers in the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA to detect crane coccidia. The authors stress that the sensitivity of detection of PCR-CE using faecal DNA was inferior to that with traditional microscopy, but was superior in solving the coccidia diversity and describe the community composition of the parasites in a host population.
Monogenean trematodes, also called flatworms or flukes, commonly invade the gills, skin, and fins of fish. Monogeneans have a direct life cycle (no intermediate host). Gyrodactylus and Dactylogyrus are the two most common genera of monogeneans that infect freshwater fish
Digenean trematodes have a complex life cycle involving a series of hosts. The genus Posthodiplostonum has caused mortalities in baitfish.
Nematodes, also called roundworms, occur worldwide in all animals. They can infect all organs of the host, causing loss of function of the damaged area.
Camillanus and Capillaria: Camillanus protrudes from the anus of the fish which makes identification easier. Camillanus and Capillaria are the most frequent infestations of fish.
Cestodes, also called tapeworms, are found in a wide variety of animals, including fish. The life cycle of cestodes is extremely varied with fish used as the primary or intermediate host. Cestodes infect the alimentary tract, muscle or other internal organs.
One of the most serious adult cestodes that affect fish is the Asian tapeworm, Bothriocephalus acheilognathi. According to Bean and Bonner 2010 the Asian fish tapeworm Bothriocephalus acheilognathi in the Rio Grande raised concern about imperiled fishes. The prevalence of Bothriocephalus acheilognathi infestation was found to be 15% in samples of red shiners in January-March and December and below 10% during April-June and October. The authors stress that over 50% of the Rio Grande fish fauna in Texas are considered imperiled. A new stress caused by the Asian fish tapeworm in combination with reduced water quantity and quality and increased habitat fragmentation is of concern.
Parasitic crustacea are increasingly serious problems in cultured fish and can impact wild populations.
Ergasilus: Ergasilus infestations affect the gills of freshwater fish, commonly seen in warm weather. Dezfuli et a. 2011 assessed the immunobiology of sea bream, Sparus aurata L. infected with the important parasitic copepod Ergasilus sp. Their study revealed that the sea bream respond to massive infections of Ergasilus sp.sending mast cells and their antimicrobial peptides (AMPs).
Lernaea , or anchor worm , is a common parasite of goldfish and koi. Hemaprasanth et al. 2011 studied the susceptibility of fingerlings of different species of carps to Lernaea cyprinacea infection. Cyprinus carpio, Labeo rohita and Labeo calbasu were found to be resistant to Lernae infections in monocultures, but only Labeo calbasu resisted to the infection when the carps were reared under polyculture conditions.The authors concluded that Labeo calbasu is the most resistant to Lernaea cyprinacea infections. Monoculture of the discussed carp species are suggested to control this parasite in culture ponds.
Freswater lice Argulus siamensis: According to Saurabh, Mohanty and Sahoo 2011 there are no suitable measure known to control the crustacean ectoparasite, Argulus which threatens carp cultures. The authors looked at the different expression of TLR 22-like, lysozyme G, β2-microglobulin genes, CXCa, lysozyme C, TNFα and complement component 3 (C3) between uninfected control and different degrees of lice infected fish. The majority of the genes showed down-regulation in kidney tissue whereas up-regulation in liver and skin tissues except C3 in Argulus-infected fish. The authors concluded that infection with Argulus siamensis result in immune gene expression changes in tissues situated away from the site of parasite attachment and feeding. This knowledge may be important to develop a control strategy for Argulus infections.