You should post a pic if you can, but I think it's safe to say it's fungal.
I have extremely healthy Harlequins, but my water parameters are near perfect. They are said to be sensitive to water conditions, so it might be something in your water chemistry.Make sure you're doing your routine maintenance, you have no ammonia or nitrites. Low nitrates. Decent pH, etc. Make sure your temperature is in the ideal range as well. Usually a fungal thing is a sign of fish stress.
If it's not too severe than try Pimafix. I've had great luck with that stuff. But if it's pretty severe you might do well for some of the more hardcore treatments, such as the Mardel Labs products like MarOxy, Maracyn, etc.
Good luck, as Harlequins are a joy and I hope this works out.