David Scott Smith, 66, and Travis Shane Smith, 32, are charged with reckless arson over the Caldor fire which started on 14 August.
Five people were injured and about 1,000 homes and other buildings were destroyed in the blaze which spread across three Northern California counties, covering more than 346 square miles (900 square kilometres).
The fire forced tens of thousands to evacuate the resort town of South Lake Tahoe before it was contained in October.
Both men were also charged with illegal possession of a firearm silencer and Travis Shane Smith is charged with illegal conversion or manufacture of a machine gun.
The criminal complaints do not specify how the machine gun and silencer tie into the fire.
Mark Reichel, the attorney for both men, said previously that the two were near where the fire started and called 911 to report flames.
"Neither one has ever been in trouble with the law in their life. They're very law-abiding people," he said.
David Smith (left) and his son Travis Shane Smith, have pleaded not guilty to an arson charge. Pic: AP
A firefighter lights a backfire to stop the Caldor Fire from spreading near South Lake Tahoe. Pic: AP
https://news.sky.com/story/california-father-and-son-plead-not-guilty-to-starting-wildfire-that-saw-1-000-homes-destroyed-12492378
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