State police charged Alfonso Frank Frazetta, 52, of Marshalls Creek, with theft, burglary and trespass after they say he was caught loading the artwork into his trailer and SUV.
"Some of these paintings are worth a million a piece," said Monroe County District Attorney David Christine.
The elder Frazetta, 81, is renowned for his work on characters including Conan the Barbarian, Tarzan and Vampirella. He was in Florida at the time of the theft.
His son's motive may stem from a family feud over the master illustrator's assets, according to a law enforcement source who spoke on condition of anonymity because it is still early in the investigation.
Frazetta was arraigned and sent to the Monroe County jail. Bail was set at $500,000. Officials didn't know whether he had a lawyer yet.
Police said that Frazetta and another man used the backhoe to enter the Frazetta Art Museum in the Pocono Mountains region on Wednesday afternoon, tripping a burglar alarm.
A trooper who responded said Frazetta claimed he had been instructed by his father "to enter the museum by any means necessary to move all the paintings to a storage facility," according to a police affidavit.
The elder Frazetta told police that his son did not have permission to enter the museum or to remove any artwork. Frank Frazetta's attorney, Gerard Geiger, said the stolen paintings were insured for $20 million, according to court documents.
Geiger said his client, who spends the winters in Florida, did not wish to comment yet.
"I don't know why Frank Jr. allegedly did what he did but it's part of the ongoing investigation with the state police," he told The Associated Press.
Police say charges are pending against a second suspect.