Coral Disease & Troubleshooting Guide: RTN, STN, Brown Jelly, Bleaching & More

1. Diagnosis Framework

Most coral problems trace to one of four categories [1]. Identifying the category drives treatment more reliably than chasing specific disease names [1]: [4]

2. RTN (Rapid Tissue Necrosis)

Rapid Tissue Necrosis is the SPS keeper’s nightmare [3]. Acropora and other SPS lose tissue from the base outward, leaving stark white skeleton behind [4]. A healthy colony can become 100% dead in 24–48 hours [3].

Symptoms

• White skeleton appearing at the colony base, spreading upward and outward [5]
• Tissue visibly sloughing off in strands
• Speed: 24–48 hours from first visible damage to complete colony death [6]
• Most severe in Acropora; less common in Montipora and PSP corals [7]

Causes

• Alkalinity swing — the most common trigger [8]. Alk dropping below 7 dKH or jumping above 10 in a 24-hour period regularly causes RTN. [9]
• Temperature shock — sudden >1°C change.
• Bacterial pathogen — some RTN cases test positive for Vibrio and similar bacteria. [10]
• Allelopathic stress from adjacent leather corals or new tank additions. [11]

Treatment (Time-Critical)

3. STN (Slow Tissue Necrosis)

Slow Tissue Necrosis is RTN’s less dramatic cousin [4]. Same general pattern — tissue loss from the base outward — but progressing over weeks rather than hours [3].

Symptoms

• Gradual tissue recession over 1–4 weeks
• Brown algae sometimes colonizing the exposed skeleton
• Coloration fades before tissue actually retracts
• Common in mature SPS colonies under chronic mild stress [5]

Causes

• Chronic parameter instability — alkalinity drifting up and down by 0.5–1 dKH over weeks. [6]
• Nutrient extremes — either ULN starvation or chronic high nitrates. [7]
• Inadequate flow for that colony’s placement.
• Persistent allelopathic stress from a softie or aggressive neighbor. [8]

Treatment

You have weeks, not hours, so the approach is gentler [9]. Stabilize parameters at consistent values (don’t chase “optimal” numbers), confirm nutrient levels in the moderate range (NO3 2–8 ppm, PO4 0.03–0.08 ppm), and improve flow if necessary [10]. Mild STN often reverses within 4–8 weeks once the underlying issue is fixed [11]. Severe STN that has consumed more than 60% of a colony usually requires emergency fragging. [12]

4. Brown Jelly Disease

Brown jelly disease (BJD) is the LPS keeper’s parallel to RTN [13]. A slimy brown coating spreads across the affected coral, consuming tissue beneath it [14]. Most common on Euphyllia (torches especially), and on brain corals after physical damage [4]. [3]

Symptoms

• Brown, slimy, mucous-like substance spreading across coral tissue [15]
• Tissue beneath the jelly dissolves over 1–7 days [16]
• Often follows physical damage (fragging, shipping, falling), water quality crash, or aggressive sweeper sting [1]
• BJD is a community of bacteria and ciliates, not a single pathogen [2]

Treatment

5. Coral Bleaching

Bleaching is the loss of symbiotic zooxanthellae from coral tissue [13]. The coral fades from its normal color to white or pale tan, but the tissue itself remains intact — bleached corals are not dead, just severely stressed and now relying entirely on feeding [5]. [1]

Symptoms

• Coloration fading from vibrant to pale or white [14]
• Underlying tissue still visible (skeleton not exposed)
• Polyp extension reduced
• Coral still alive — intact tissue but no algae [15]

Causes

• Light shock — new coral moved to higher PAR without acclimation, or fixture intensity increased. [16]
• Temperature spike — sustained temp above 28°C is the classic bleaching trigger. [1]
• Ultra-low nutrients — in ULN tanks, corals can bleach from zooxanthellae starvation. [2]
• Alkalinity above 10 dKH — chronic high alk causes bleaching, especially in SPS. [3]
• Sudden parameter change of any kind.

Recovery Protocol

• Move to lower-PAR zone — place the bleached coral lower in the tank, in shaded rockwork. [4]
• Increase feeding frequency — bleached corals have no algae, so they need exogenous nutrition [5]. Daily target feeding for 4–8 weeks accelerates recovery. [6]
• Stabilize parameters — halt all parameter shifts; aim for steady consistent numbers. [7]
• Wait 8–16 weeks — zooxanthellae populations recover from the coral’s baseline [8]. Color returns gradually.
• Don’t move the coral around — further stress slows recovery. [9]

6. Black Band Disease

Black band disease (BBD) is a band of cyanobacteria-led microbial mat that advances across coral tissue, killing it as it moves [6]. Less common in aquariums than RTN or brown jelly, but distinctive enough to require its own treatment [10]. [4]

Symptoms

• Dark brown to black band visible on the coral surface, 5–30 mm wide [11]
• Healthy tissue on one side of the band, exposed dead skeleton on the other [12]
• Band advances 3–15 mm per day
• Most common on Trachyphyllia, Lobophyllia, Goniopora, and other massive LPS [13]

Treatment

• Mechanical removal — use a syringe or baster to wash the band off in a separate container. [14]
• Iodine dip — Lugol’s iodine solution for 5–10 minutes can kill remaining bacteria. [15]
• Cover with kalkwasser paste — some reefers paste a small amount of kalkwasser slurry over the band to chemically kill the bacteria mat [16]. Risk: damage to surrounding tissue.
• Strong protein skimming in the display tank helps prevent transmission. [1]

7. White Band & White Pox

White band disease and white pox primarily affect wild Acropora reefs and are less common in aquariums, but worth knowing [2]. They present as sharply-defined white patches that advance across the colony, usually with no slime or jelly accompanying the tissue loss (distinguishing them from RTN with brown jelly contamination). [3]

Treatment overlaps with RTN: identify, frag healthy tissue, dip, quarantine [4]. The bacterial agents involved (Vibrio family) are sensitive to high-quality water with active skimming [5]. Many aquarium “white band” cases are actually RTN with secondary algae colonization on the exposed skeleton [7].

8. Bacterial Infections

A general bacterial infection often presents as a localized tissue dissolution or wound that doesn’t heal over weeks [6]. Most often follows physical damage (fragging cut not healing, fall, fish nip). [7]

• Symptoms: persistent unhealed wound, slow tissue regression from the wound site, sometimes mild brown discoloration [8]
• Treatment: dip in CoralRx or iodine, place in low-flow recovery zone, increase feeding [9]. Most heal within 2–4 weeks. Severe cases may need amputation back to healthy tissue. [10]

9. Dinoflagellates

Dinoflagellates (“dinos”) are single-celled algae that can devastate a reef tank [11]. The brown/snotty/stringy mats appear in tanks with extremely low nutrients and can suffocate corals and invertebrates [8].

Symptoms

• Snotty, stringy, brown to greenish mats appearing on rockwork, sand, and equipment [12]
• Sometimes contains visible air bubbles trapped in the mat (a giveaway) [13]
• Tank running very low nutrients (NO3 below 1 ppm, PO4 below 0.02 ppm) [14]
• Snails and other invertebrates dying in the affected zones [15]
• Diatom-like sheen but with stringy texture when disturbed [16]

Treatment

• Stop chasing zero nutrients. The cure is raising nitrate to 5–10 ppm and phosphate to 0.05–0.10 ppm via reduced skimming, more feeding, or direct dosing. [1]
• UV sterilizer — 18–25W UV running 24/7 kills free-floating dino cells. [2]
• Manual removal — siphon dino mats during water changes. [3]
• Increased flow on affected rock surfaces.
• 3-day blackout — cover the tank completely for 72 hours [4]. Kills photosynthetic dinos. Repeat after 2 weeks if needed.
• DinoX or Dinex — commercial treatments specifically for dinoflagellates [5]. Use only as a last resort and follow dosing carefully. [6]

Dino battles typically last 4–12 weeks [7]. Patience and consistency win. See the algae control guide for related coverage. [8]

10. Cyanobacteria (Red Slime)

Cyanobacteria are not algae — they’re photosynthetic bacteria [9]. The reef-tank manifestation is a red/purple/orange slimy film coating rocks, sand, and equipment [10]. Less destructive than dinos but visually unappealing and indicates excess nutrients [9].

Symptoms

• Red, purple, or maroon slime mats on substrates [11]
• Can be peeled off in sheets
• Air bubbles often trapped in the mat (similar to dinos) [12]
• Tank running high nutrients (NO3 above 15, PO4 above 0.15) [13]

Treatment

• Reduce nutrients — the cure is the opposite of dinos: lower nitrates and phosphates via improved skimmer performance, less feeding, or water changes. [14]
• ChemiClean or similar antibiotics — effective and reef-safe at proper dosing [15]. One treatment cycle kills cyano. Address the underlying nutrient cause to prevent recurrence. [16]
• Flow on affected zones — cyano hates strong flow. [1]
• Manual removal during water changes — siphon off as much as possible before treatment. [2]

11. The Treatment Toolkit

Keeping these on hand turns most coral emergencies into manageable problems instead of disasters. [3]

12. Emergency Fragging

When a colony is clearly dying and cannot be saved as a whole, the goal becomes preserving as much living tissue as possible as frags [14]. See the complete fragging guide for tools and basic technique. [15]

Decision Criteria

• RTN visible: frag immediately, don’t wait.
• STN consuming >50% of colony: frag the remaining tissue. [16]
• Brown jelly spreading despite blasting: remove healthy tissue. [1]
• Bleaching plus signs of infection: frag the healthy section if possible. [2]

Emergency Frag Protocol

1. Remove the colony from the display tank
2. Cut multiple frags from clearly healthy tissue, well past the disease boundary [3]
3. Dip each frag (CoralRx for general, Bayer for pest-related, Lugol’s for BJD) [4]
4. Mount to plugs with cyanoacrylate (or rubber band for softies) [5]
5. Place in quarantine tank, NOT back in the display until 2–4 weeks of stable health [6]
6. Sanitize tools and dispose of necrotic tissue securely [7]
7. Run carbon in the display to remove any toxins released by the dying coral [8]

13. Prevention

Most coral diseases are preventable. The reef hobby’s collective wisdom on prevention boils down to: [9]

• Quarantine and dip every new coral. See the acclimation guide for the protocol. [10]
• Stabilize parameters above all else. Pick targets and hold them [11]. Don’t chase “optimal” numbers up and down. [12]
• Test parameters at least weekly in established tanks, daily in tanks under treatment. [13]
• Maintain reasonable nutrient levels (NO3 2–10, PO4 0.03–0.10 for most mixed tanks). [14]
• Keep a quarantine tank running. Even just a 10-gallon basic tank is invaluable. [15]
• Run carbon in mixed soft + stony tanks to reduce allelopathic stress. [16]
• Plan placements with night-sweepers in mind: Euphyllia, Goniopora, chalice, and brain corals all extend long sweeper tentacles after lights off. [1]

14. Frequently Asked Questions

References

1. Reef Builders — Coral Disease Diagnosis Framework
2. Top Shelf Aquatics — SPS Coral Stability
3. Advanced Aquarist — RTN, STN, and SPS Tissue Necrosis [4]
4. Tidal Gardens — Brown Jelly Disease (BJD)
5. Reefs.com — Coral Bleaching: Causes & Recovery
6. NOAA — Black Band Disease in Corals
7. Reefkeeping Magazine — White Band & White Pox [5]
8. Bulk Reef Supply — Dinoflagellates Complete Guide
9. Reef Builders — Cyanobacteria Treatment
10. CoralRx — Coral Dipping Guide
11. Melev’s Reef — Emergency Fragging Protocol
12. Reef2Reef — RTN Troubleshooting community thread
13. Bulk Reef Supply — SPS Coral Care & Disease Prevention [6]
14. Reef Chasers — Dinoflagellate Treatment
15. Advanced Aquarist — Coral Bacterial Pathogens
16. Reef2Reef — Brown Jelly Disease Treatment community thread [7]