What are the black streaks on my roof? Many homeowners are surprised to discover that their once clean asphalt roof shingles have been slowly covered with a form of roof Algae or Mold that appears as a light discoloration and spreads down the roof toward the gutters. The black roof stains are caused by a form of algae that has been around for years, typically found in the woods on the north side of trees, or on exposed rocks; but now this black algae is termed a roof shingle algae because of the annoying discoloration on an asphalt shingle roof. The roof algae actually feeds on the crushed limestone that is present in the shingles. The roots of this Algae also works like a wick and transfers moisture into the substrate of the roof or walls. The roof algae is spread by wind and animals from roof to roof and is a challenge to prevent, but with proper attention can easily be cleaned and managed from doing damaged.