The dogs were taken sometime between Monday and Tuesday from the backyard of a house in the 2300 block of Holland Street, San Mateo police Sgt. Bob Szelenyi said.
Their owners reported the dogs missing around 5:15 p.m. Wednesday, Szelenyi said.
Tyler Hill, a San Mateo resident, was arrested about two hours later after he was found to be in possession of two of the puppies, according to Szelenyi.
Szelenyi could not release the location of the other puppies and their mother, but said all of the dogs are all right.
"There's no reason to believe any of the dogs have died," he said. Police are looking into several other possible suspects as well, Szelenyi said.
A motive for the theft remains under investigation.
The San Mateo County District Attorney's office charged Hill with one count of misdemeanor grand theft, Chief Deputy District Attorney Steve Wagstaffe said.
Hill pleaded not guilty in court today and remains in custody in lieu of $10,000 bail, according to Wagstaffe.