Are all puppies sold in pet stores from puppy mills?

I would say a good number of them come from puppy mills. When you see lots of variety of dogs in a pet shop like that, that usually means they have connections to get these dogs, and can get them again once they sell what they have. I am sure some are from backyard breeders (who will probably eventually turn into puppy mills) but either way it's not the smartest environment to buy an animal.