Amyloodinium ocellatum is a single-celled Dinoflagellate which is commonly regarded as a form of algae. Most algaes are harmless to fish although this particular species is parasitic to marine fish during a single stage of its life-cycle. An adult cyst will release up to 300 free-swimming cells called dinaspores which attach to its host or lay dormant in the aquarium/ocean bottom. They can lay dormant for periods of up to 6 weeks and are resistant to any medications in this stage. Upon hatching, the spore then searches out a new host to provide the nutrition it needs to survive. After several days of feeding on its host, the parasite will leave its host and begins the cycle all over again releasing dinaspores into the water once more.
Contrary to popular belief, Treating this parasite in a marine aquarium doesn't require medications, additions of copper or other dangerous chemicals. There are more natural and far safer methods we can utilize. What we must be aware of is that while in the cyst stage (eggs laying dormant in substrate) the parasite is resistant to medications as well as other methods of eradication. This is why oftentimes after treatment with medications, the parasite returns. The parasite can lay dormant for several weeks for as long as 6 weeks.
Knowing this, we realize that the only true method for totally ridding a home aquarium of this parasite would be to remove all fish for a period of 6 weeks. During this time, all the cysts will have hatched and being unable to find a host will have died. But once an infected fish is added to the system, the cycle starts a new. (hence, the necessity of a quarantine tank for new species for several weeks)
There is an easier way to address this problem. First, we must except that this parasite is common in most systems. That said, we must look at addressing an outbreak, not just the mere presence of the parasite. What is an outbreak? An outbreak is a noticeable attack on one or more fish. Keep in mind that a blemish or what appears to be a single parasite is not considered and outbreak. These types of occurrences are commonly handled by the fish with little or no help from the aquarist.
What should you do if you have an outbreak? Fish take in water through their bodies on a regular basis. They expel it at or about the same rate. This is called "osmosis". Parasites do the same as well. However, parasites are far more fragile and are effected at a much higher rate by changes in salinity. Lower salinities can be harmful to both fish and parasites, not to mention invertebrates. There is a safe zone for fish and inverts that will effectively help the aquarist attack the attached parasites. The lower level will still effect your fish and invertebrates but to a much lesser extent. They will be stressed mildly but will be able to cope with this lower salinity. (don't be alarmed at corals and other invertebrates contracting during treatment)
Temperature increases help to speed up organisms metabolism. This also helps in combating the parasite. An Increase in temperature is directly related to a higher rate of osmosis. That being said, lets look at a possible course of corrective actions for dealing with an outbreak.
Over a period of several hours, slowly raise your temperature to about 84 degrees and lower your salinity to 1.020 to 1.018. This will cause the parasites attached to your fish to take in much more water than they can expel causing them to literally explode. They will die and fall off their host. Maintain this temperature and salinity for a period of 2 - 3 days and then slowly (over several hours) bring your temperature and salinity back to normal. (to raise your salinity, increase agitation of water at the surface and/or position a fan to blow across the water's surface). Keep in mind that the parasite will still be in the system in cyst form in the substrate (the form in which it is resistant to treatment) but this will allow your fish to build up a strong defense system against them. As long as you keep your system healthy, you shouldn't experience any additional significant problems.
Your sensitive invertebrates will be affected though only mildly. These changes normally happen on many natural reefs as well due to run-off and extensive rain-fall. After the treatment has been completed, you can remove any aquarium covers and utilize a fan to blow across the water's surface to bring your salinity back into natural parameters over a couple of days as well as returning your temperature to normal parameters. This technique has worked successfully for me on several systems and I have not had an outbreak since in any system treated in this manner. Keep in mind that I have not introduced any new specimens to these systems as well.