sounds like some cyano bacteria (red). what are your nitrate and phosphate levels? having elevates levels of those can cause it. also, increacing water movement in those ares will prevent it too. the better your oxygen levels in your water the less cyano you will get.
Also, how old is the tank? You'll go through various blooms in a new tank that are normal. If it is more brownish than red, it may be diatoms. In addition to what pickupman said, you can toss in a clean up crew and let time pass.
I've also read that making sure your alkalinity is in line will help assuming it is cyano. As already said, a new tank will usually go through various blooms before straightening itself out.
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