One of the growing trends that I have seen (and experienced) is that flukes are becoming more and more common in the hobby. It used to be that fluke were more common on only certain types of fish, but more and more it seems that all fish can easily get them, or at least that has been my experience.
Flukes are a type of parasite with the broad group of gyrodactylus parasites. There are two common types of flukes, the ones that infect the skin of the fish (dactylogyrus trematodes), and the second that will infect both the skin and gills of the fish (monogenenean trematodes).  Both can be very hard (if not almost impossible) to visually see on the fish until very advanced stages. While attached to the fish, they will feed on the tissues they are attached to. At some point they will start releasing eggs which will fall and lay dormant within the aquarium for about a week.  They will hatch , releasing a free floating / swimming larva. This larva will survive for two or three days without attaching to a host before dieing. Typically the larvae will attach itself to either the gills or skin of the fish. Once attached, the larva will develop into a worm and releasing eggs continuing the life cycle. This final stage can last for about a week, maybe a little longer

Common Symptoms to look for:

The below list is the most common symptoms that you will find.  You may notice one or many of the symptoms listed below:

1 Cloudy eyes
2 Rapid breathing
3 Fraid fins
4 Excessive slim coat production
5 Loss of appetite or even completely stopping to eat
6 twitching/shaking the head from side to side almost like it was trying to shake something off its head
7 discolored blotches on the fish which can even look a lot like velvet some times
8 Flashing against objects in the aquarium with periods of almost no activity
9 White to almost translucent spots on the fish that look almost like the ick virus, but are larger and not as close together.

Treatment Options:
1- Fresh water dips
While many hobbyists still successfully use freshwater dips, I do not like nor do I recommend fresh water dips. When completed incorrectly, they can cause more harm than good to an already sick fish. Additionally, with many of the new(er) medications available today that are a lot more effective and less harmful and less stressful to the fish, I feel fresh water dips are no longer required.
2- Treatment with medication in a QT set-up
This is my preferred method and is the one that I have obtained the most success with. I would recommend a treatment with Prazi-pro. This medication is safe to use in reef tanks with SPS corals and carpet anemones, and is also safe to be used in a QT set-up with copper based medications. However, they key to being able to successfully treating flukes is catching the symptoms early enough for the treatment to work. If the infection has spread to much through the gills, or the fish is no longer eating, you have a lower chance of successfully treating the fish.  You also have to keep in mind, is that by treating a infected fish in a QT step-up or in a medicated treatment dip, you are not dealing with any of the parasite’s eggs that could be in your main tank waiting to hatch and infect / re-enfect your fish.  You may have to consider treating  your whole system.
The only caution to using prazi-pro in a display tank is that it will have an effect on worms (like flat worms) as well as some of the more sensitive filter feeders like coco-worms.

Preventative Measures
I always QT any fish I get before adding them to my display tank. As fish can carry flukes without actually becoming infected, I always use a preventative treatment of prazi-pro while in QT. While there are many medications out there that work on flukes, I have found prazi-pro works the best and it has the least side effects. Copper based medications will not work on flukes.

How did flukes get into my aquarium?

In short, they will have to be brought into your set-up by you.  Typically they will get into your setup through:
1 An infected fish
2 On live rock from a infected set-up
3 On a coral form a infected set-up
4 In water added to your tank from an infected set-up
Poor water quality and / or environment stress will allow fluke to thrive and really take hold in your set-up.

Just a Word on Using Medications
1 Make sure your salinity is at least at 1.025 when using meds. All meds have a stronger than intended impact when used at lower levels of salinity
2 If treating with Praz-pro, remove your skimmer cup but leave the skimmer running. The use of praz-pro will make your skimmer go nuts. It will produce a truly amazing amount of bubbles like you have never seen before. You want to still have your skimmer running to keep the oxygen levels high in the water as some medications like praz-pro can lower the amount of oxygen in the water which is something you want to avoid.
3 Don’t forget to remove any type of carbon that you have running in your system
4 Fresh water dips will only remove the flukes from a infected fish, and not the flukes which are laying dormant within your set-up
5 Poor water quality and environmental stress will make most medications close to being useless