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Prevention beats treatment
Almost every pest and disease in a reef tank arrived on something: a fish, a coral frag, a piece of rock, a snail, even water from a store bag. The single most effective defense is a quarantine tank and a routine for every new arrival. Many treatments that work well in a bare quarantine tank (copper, antibiotics, hyposalinity) cannot be used in a reef display without killing invertebrates, corals or the biological filter.
This guide covers the problems that come up most often. It isn't veterinary advice. Always confirm identification and follow medication labels.
Marine ich (Cryptocaryon irritans)
What it is. Marine ich, or "crypto", is caused by the ciliate parasite Cryptocaryon irritans. It's unrelated to freshwater ich (Ichthyophthirius) despite the name.
Signs. Small white spots like grains of salt on fins and body, scratching on rock or sand ("flashing"), rapid breathing, cloudy eyes, and loss of appetite. Surgeonfish (tangs) are notoriously susceptible. Gill infestations can kill fish with few visible spots.
Life cycle. This drives every treatment decision. The feeding stage (trophont) lives in the skin and gills for several days, drops off, and forms a cyst (tomont) on rock or sand. Inside, it divides into hundreds of free-swimming theronts, which must find a fish within about a day or two or die. The cycle is temperature-dependent, and some tomonts take weeks to hatch.
Treatment options (in quarantine, never the reef display):
- Copper. The most common treatment. Maintain therapeutic level for the product: about 0.5 ppm for Seachem Cupramine (per Seachem's directions) (ionic copper) or 1.5–2.5 ppm for chelated products such as Endich Copper Power (per the manufacturer), measured with a test kit matched to the product, typically for at least 14 days. Copper is lethal to invertebrates and binds to rock and sand, so it must never be used in a reef tank.
- Tank transfer method (TTM). Move fish to a clean, sterile tank every three days for four transfers, so tomonts are left behind before they can hatch. Medication-free, but labor-intensive.
- Hyposalinity. Holding salinity around 1.009 SG (about 12–14 ppt) for about 4–6 weeks (commonly cited hobby protocol) prevents the parasite from completing its cycle. It requires a very accurate refractometer and does not work for all fish.
- Chloroquine phosphate is used by experienced hobbyists for resistant cases.
The display tank. To eradicate ich from a display, remove all fish to quarantine and leave the display fallow (fishless) so the parasite dies off with no host. A commonly recommended fallow period, based on the parasite's life cycle, is about 72–76 days; that is hobby guidance rather than a guarantee, and some keepers go longer. Corals and invertebrates can stay in. Products sold as "reef safe ich cures" generally have weak evidence behind them.
Acropora-eating flatworms (AEFW)
What they are. AEFW are small polyclad flatworms (Prosthiostomum acroporae, originally described as Amakusaplana acroporae) that eat Acropora tissue. They are well camouflaged, often matching the coral's color.
Signs. Bite marks that look like small semicircles of missing tissue, slow tissue loss with no chemistry cause, and clusters of brown or golden egg masses on bare skeleton, usually at the base of branches. Shining a flashlight at night or blowing the coral with a turkey baster can reveal worms.
Treatment. Dip affected colonies in a coral dip formulated for flatworms. Because dips kill adults but not eggs, repeat dips are needed as eggs hatch, commonly weekly for several weeks. Scrape or cut off any visible egg masses. Some hobbyists treat entire systems with veterinary anthelmintics, but these are off-label and can cause flatworm die-off that pollutes the water. Hobbyists report that some wrasses (for example certain Halichoeres species and the sixline wrasse, Pseudocheilinus hexataenia) eat AEFW, which may help but rarely eradicate them.
Prevention. Dip and inspect every Acropora, cut off the base of new frags, and quarantine new Acros for several weeks with repeat dips.
Dinoflagellates (dinos)
What they are. Dinoflagellates are single-celled algae-like organisms. Several genera cause aquarium outbreaks, including Ostreopsis, Prorocentrum, Amphidinium, Coolia and others. Some produce toxins that kill snails and other invertebrates.
Signs. Brown, golden or greenish snotty films with stringy strands and trapped air bubbles. They often vanish at night and return when lights come on. They frequently appear in new tanks and in tanks where nitrate and phosphate have bottomed out.
Identify first. Look at a sample under an inexpensive microscope (100–400×). Treatments differ by genus. For example, UV sterilization helps species that spend time in the water column (such as Ostreopsis), but not sand-dwelling species such as Amphidinium.
Treatment.
- Raise nutrients. Bring nitrate and phosphate up to detectable levels by feeding more or dosing nitrate and phosphate. See our nutrient guide. This is the foundation of most successful approaches.
- Stop or reduce export such as GFO, carbon dosing and heavy skimming while you rebalance.
- Add competition. Bottled bacteria, copepods and phytoplankton can help outcompete dinos.
- Blackouts of a few days help some outbreaks but rarely cure them alone.
- Siphon films out through a filter sock, and avoid big water changes, which can feed them fresh trace elements.
Cyanobacteria (cyano)
What it is. Cyano, "red slime", is a photosynthetic bacterium, not algae. Colors range from deep red and burgundy to green and black.
Signs. Slimy mats on sand and rock that peel off in sheets, often with bubbles. It typically grows in low-flow areas.
Causes and fixes. Cyano is associated with low flow, detritus, imbalanced nutrients (it can fix its own nitrogen, so it thrives where nitrate is low but phosphate is available), and old or mismatched lighting. Increase flow over affected areas, siphon mats out, clean detritus, and rebalance nitrate and phosphate. Raising a near-zero nitrate often helps. Erythromycin-based products such as Chemiclean can clear outbreaks, but they are antibiotics: follow the dose exactly, keep oxygen high (they can lower dissolved oxygen), and fix the root cause or it will return.
Aiptasia
What it is. Aiptasia (glass anemones, genus Exaiptasia) are small brown anemones that hitchhike on rock and frags. They sting corals, spread quickly, and regrow from tiny fragments of tissue.
Treatment.
- Injection products such as Aiptasia-X or a kalkwasser paste kill individual anemones. Apply to the base and cover the oral disc so the anemone doesn't retract and spread.
- Peppermint shrimp (Lysmata wurdemanni and L. boggessi) eat aiptasia, though individual shrimp vary, and some will sample corals.
- Berghia nudibranchs eat only aiptasia and are a very effective biological control. They starve once aiptasia is gone, and some fish and shrimp eat them.
- Aiptasia-eating filefish (Acreichthys tosaensis) are effective but may nip soft corals and zoanthids.
Don't scrape or cut aiptasia: fragments can regenerate into new anemones.
Other problems to know
- Velvet (Amyloodinium ocellatum) is a fast, often fatal fish parasite that looks like fine gold dust. It needs immediate copper or chloroquine treatment in quarantine.
- Brooklynella and Uronema are ciliate infections, especially in clownfish and in stressed fish.
- Red bugs on Acropora, Montipora-eating nudibranchs, zoanthid-eating nudibranchs and sea spiders all call for dips and inspection.
- Vermetid snails produce mucus nets that irritate corals.
- Green hair algae and bubble algae respond to nutrient control, manual removal and herbivores such as emerald crabs, urchins and tangs.
A simple quarantine plan
- Fish: a separate tank with a heater, filter or seeded sponge, and PVC hiding places. Observe or prophylactically treat for at least several weeks (many people treat for ich and velvet, and some for flukes and internal parasites).
- Corals: dip, inspect, remove plugs or bases where possible, and ideally hold in a coral QT for several weeks with repeat dips.
- Invertebrates and rock: inspect and hold separately. Invertebrates cannot be treated with copper.
A tank kept with stable parameters is also more resistant. Stressed fish get sick more easily. Keep your logs and use the dosing calculator to keep chemistry steady.
Summary
Quarantine is the best treatment. For ich, treat fish in quarantine with copper, TTM or hyposalinity and leave the display fallow for about 72–76 days. Dip and inspect Acropora for AEFW, and repeat dips to beat the eggs. Raise nutrients and identify the species for dinos. Fix flow and nutrients for cyano. Use injection or biological control for aiptasia.
Frequently asked questions
Can I treat marine ich in my reef tank?
Not effectively. Copper and hyposalinity kill invertebrates and corals. Move fish to a quarantine tank for treatment and leave the display fallow for about 72 to 76 days.
How do I know if I have dinos or cyano?
Cyano forms slimy mats that peel off in sheets. Dinos form stringy, snotty films with bubbles that often disappear at night. A microscope gives a definite identification.
How do I get rid of AEFW?
Dip affected Acropora in a flatworm-rated coral dip, remove egg masses, and repeat dips weekly for several weeks because eggs survive dips.
What eats aiptasia?
Berghia nudibranchs, peppermint shrimp (Lysmata wurdemanni and L. boggessi) and the aiptasia-eating filefish Acreichthys tosaensis.
What causes dinoflagellates in a reef tank?
Outbreaks are common in new tanks and in tanks where nitrate and phosphate have dropped to zero. Raising nutrients is the foundation of most treatments.
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More reef science guides
- Alkalinity, calcium & magnesium
- Nitrogen cycle & cycling
- Nitrate & phosphate
- Salinity & RO/DI
- Lighting & PAR
- Coral types & care
- Reef conservation & science
- Coral symbiosis & Symbiodiniaceae
- Coral bleaching science
- Ultra-low nutrient research
- Ocean acidification & calcification
- Coral restoration & microfragmentation
- ICP testing & trace elements
Ranges are common hobby targets compiled from reef chemistry literature (including Randy Holmes-Farley's articles), hobby consensus and manufacturer documentation. They're not rules. Last reviewed 2026-10-15.