What kind of lighting do you have? Have you tested nitrates? How often do you change water and how much? Do you have live plants in the tank?
A lot of wastes can accumulate between the rocks unless you clean them well often. Even if your cycle can take care of the ammonia and nitrites caused by the dirt, nitrates can get very high which can easily lead to algae blooms.
Brown algae also thrives in low/bad light conditions. In low light conditions plants grow slower which leaves more nutrients for the brown algae to use. Brown algae can also benefit from "bad light", meaning there are wave lengths that plants aren't able to use, but algae has no problem with it. If your light pulps are old then it might be time to get new ones.
Third thing that causes brown algae blooms is that there might be too much phosphates or silicates in your water. But if this just appeared now, then it's probably because of the other things.
I'd suggest cleaning out all the algae you can, cleaning the tank (but be careful not to crash your cycle), getting some fast growing plants, testing the water often and making sure the nitrates stay at around 20 ppm max.