The group's website says the term Hutaree means "Christian warrior" and characterises the group as "preparing for the end time battles to keep the testimony of Jesus Christ alive".
Federal authorities arrested eight people over the weekend during raids in Michigan, Ohio and Indiana.
The leader's son, 21-year-old Joshua Stone, was arrested late on Monday in a former militia training area near a church in rural Wheatland Township, Michigan, the local Detroit Free Press newspaper reported.
The militia members face charges of seditious conspiracy, attempted use of a weapon of mass destruction, teaching the use of explosive materials and possessing a firearm during a crime of violence.
Eric Holder, the US attorney-general, called the alleged plot an "insidious plan" by anti-government extremists".
"Thankfully, this alleged plot has been thwarted and a severe blow has been dealt to an dangerous organisation that today stands accused of conspiring to levy war against the United States."
Prosecutors say the militia was led by 45-year-old David Brian Stone, who was among those arrested.
Stone had allegedly begun gathering materials for improvised explosives, taught members how to use them and was planning to begin searching for a target in April, officials said.
The accused face a maximum sentence of life in prison in convicted.