The following is a copy from: http://www.thisoldhouse.com/toh/asktoh/question/0,,1549864,00.html

Q: My roof is streaked with black stains. Is there anything I can do to get rid of them? The shingle manufacturer says that staining isn't covered by the warranty because it doesn't affect the performance of the shingles. 

A: The dark streaks are a type of algae that lives off the minerals in some types of roof shingles. Algae thrives in moisture, so it's seen most often on shaded or north-­facing roof slopes that don't get a lot of direct sun.

While it's true that algae doesn't damage roofing, it sure looks bad. To get rid of it, use a pump sprayer to wet down the roof with a mix of one part bleach to two parts water. Bleach will damage foundation plantings, so rinse them well with fresh water before you start and after you're done.Then scrub the surface gently with a soft window—washing brush mounted on a telescoping extension pole. Don't use a pressure washer, which could damage the shingles. Also, do this work from the safety of a ladder or from the ground, not by climbing on the roof.

To stop the algae from returning, mount zinc or copper strips near the roof ridge. Then, every time it rains, the water that washes over the strips' exposed edges will pick up ions from the metal and inhibit the algae from regaining a foothold. And when it's time for a new roof, look for shingles with algae—resistant granules and the best warranty you can find.