Usually algae.

Watch out for folks trying to use a pressure washer to remove the stains.

It is very easy to strip a lot of the grit from the shingles, shortening their life.

My DH has been outside this last week dealing with the roof algae. He has used a pumpup sprayer with a water and bleach combination to spray the roof down. Then he rinses with the water hose.

I'm not sure, but I think he will finish up by sealing the roof again. Being a southerner, I'm not familiar with the issues that roofs encounter in a cold climate.

His house is a cape, the roof is also gray. It looks better now that he has finished the bleach job. I have no idea what other remedy you might try than this one. But I'd do it quickly before the weather gets really ugly.

Thank you, ladies and gentlemen for the responses.
I'm 70, maybe too old for scaling these steep roofs.
The resealing of the roof is vital, else this algae will return, with a vengeance.
Bleach can do a quick and effective job on concrete, which can look so pretty after being cleaned.

If these are asphalt shingles, I'm not aware of any way to "reseal" them. If you do get the algae off, a strip of copper or zinc at the roof peak will keep it from returning. Many shingle manufacturers offer a 10 year warranty aginst algae. After that you're on your own. Learning to live with it is probably the best option.

Thank you, Mainegrower.
If these shingles are over 15 years old, I'll plan on replacing them.
Records are important with the house , man, or car. In this case, my wife knows(more or less) the PO.
Its a rather nice house from the 50s or 60s in the "low price" field, that is up for auction 20 days from now.

Everybody saying its mold.My hubby is a contractor he thinks its failure in the way they colored the shingles.the guy he buys from told him how its done.Youre seeing alot of this.