They were the first charges to allege sedition, defined as attempting “to overthrow, put down or to destroy by force the government of the United States”.
The offence can can carry a sentence of up to 20 years in prison.
Rhodes, the most high profile of 725 people charged so far for allegedly taking part in the attack on the Capitol, founded the Oath Keepers, a militia that claims to be defending the Constitution of the United States.
Its membership is largely made up of current and retired military and law enforcement officials.
The indictment portrays Rhodes as a ringleader who warned his members to prepare for a "bloody and desperate fight" to prevent Democrat Joe Biden from becoming president.
It says he helped rally his members to go to Washington and played a key role in organizing and helping stage logistics for the group, including the establishment of so-called "quick reaction force" teams that stashed firearms outside the city limits.
The indictment also says Rhodes spent thousands of dollars stockpiling gear and weapons, including an AR-15 rifle, night vision goggles and ammunition.
A lawyer for Rhodes said he was arrested by the FBI at his home in Granbury, Texas, on Thursday. He has not yet entered a plea in the charges.