Yes I am afraid you have dinoflagellates. There are couple different treatments out there I believe, but generally it is the result of too much nutrients being trapped in your water, not enough live rock,and/or there not being enough flow. What happens is that the dino's sort of "take over" the job of consuming nutrients that is normally done by the beneficial bacteria and algae that are normally in our live rocks and our refugiums. I had them for a while but successfully got rid of them.
My strategy was: Turn off your lights for a few days(since they disappear without light energy) and skim VERY wet(emptying your skimmer cup multiple times a day) for the days while you have your lights off. This will help you get rid of as many nutrients as possible(which the dinos consume for food). I don't recommend water changes as they seem to exacerbate the dino problem for some reason. Next, since dino's are a symptom of a larger problem, you'll have to change some things around in your tank. You want to increase flow, and try to get rid of "dead spots" in the tank. You also want to make sure that your rock structure is open enough and actually has flow moving through it. For example, if you just had a large pile of rock in your tank, and no powerheads pointed at it, then you aren't going to get much flow THROUGH your live rock. Lack of flow is detrimental to your beneficial bacteria, and will contribute to allowing the dinoflagelates to get "the upper hand." So in summary, turn out lights and skim heavy for a few days to get rid of nutrients, and increase flow through your rock work by "opening up" your aquascape, and repositioning/adding more powerheads.
Edit to add that you also may want to replace your lightbulbs if they are old. Spectrally shifted old bulbs may also contribute.
Peace,
Jesse
