Dinos usually diminish when the lights are out, then come back when the lights are on. You didn't provide too much of a description so it's hard to say, but dinos sound like a possibility. There's several methods to get rid of them, all with varying degrees of success. Personally I went with a mix of increasing my magnesium to 1500ppm, stopping water changes, and started dosing a carbon source. I can't vouch for any one of those in particular but they seemed to function well enough for me. Essentially anything you can do to improve the PO4 and NO3 levels will help.
Dinos are a pain in the neck, so for your sake I hope that it's something else.