This could mean your roof has vegetation, fungus, mold, or algae growth, or that the shingles protective granules have been lost.
This doesnt mean you need to replace your roof, but these stains can reduce curb appeal.
Cleaning the shingles is an option, but that could shorten their life. Fortunately, StainGuard protection is available on many GAF Shingles, including Timberline Cool Series Shingles, Timberline Natural Shadow Shingles, and Timberline ArmorShield II Shingles.
(StainGuard protection is available only on shingles with StainGuard-labeled packaging. See GAF Shingle & Accessory Ltd. Warranty for complete coverage and restrictions.)