Pete Musico, 42, and Joseph Morrison, 26, were arraigned at the Jackson County District Court in Michigan on Thursday afternoon on multiple felony charges related to the alleged plans.
Mr Musico and Mr Morrison have been charged with threat of terrorism, gang membership, providing material support for terrorist acts and carrying or possessing a firearm during the commission of a felony.
On Thursday, the Federal Bureau of Investigation (FBI) announced that it had charged 13 militia members over the plot to kidnap the governor and target other law enforcement members.
The FBI said the men planned to capture Ms Whitmer before 3 November’s national election and “try” her in Wisconsin.
Six men were arrested following a raid at a home in Detroit on Thursday morning, while seven more, who are part of the rightwing militia group, the Wolverine Watchmen, were arrested later that day.
Mr Musico and Mr Morrison, co-founders of the militia, have been accused of providing training to group members on Mr Morrison’s property in Munith, Louisiana.
They were recruited to help train the other men to kidnap Ms Whitmer, and allegedly planned to attack the Michigan State Capitol to incite a “civil war”.
The men have also been accused of carrying out surveillance on bridges they allegedly planned to blow up and collecting addresses of law enforcement agents they planned to kill, according to Munith Live.
At the arraignment on Thursday afternoon, magistrate Fred Bishop said that he set the bail at $10m because he believes the pair are a danger to the public.
In a statement following the arrests, attorney general Dana Nessel said: “There has been a disturbing increase in anti-government rhetoric and the re-emergence of groups that embrace extremist ideologies.”
She added: “These groups often seek to recruit new members by seizing on a moment of civil unrest and using it to advance their agenda of self-reliance and armed resistance.
“This is more than just political disagreement or passionate advocacy. Some of these groups' mission is simply to create chaos and inflict harm upon others.”
Mr Musico and Mr Morrison are scheduled back in court on 21 October for preliminary examinations in front of Jackson County District judge Michael Klaeren.
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