The five face 16 felony charges relating to an armed standoff the Bundys and their supporters had with the federal government in 2014.
Ryan Payne, who participated in the Oregon wildlife occupation, and Peter Santilli were also charged, authorities say.
"Persons who use force and violence against federal law enforcement officers who are enforcing court orders, and nearly causing catastrophic loss of life or injury to others, will be brought to justice," U.S. Attorney Daniel G. Bogden said.
Cliven Bundy was denied bail on Tuesday after a judge in an Oregon federal court determined that he was a flight risk, said Natalie Collins, a spokeswoman for the U.S. Attorney's Office for the District of Nevada. Bundy is scheduled to be back in court Friday.
, Bundy was charged with six counts in that 2014 showdown against federal land managers on the open range where his cattle grazed and fed.
The federal Bureau of Land Management and local authorities backed down in the face-off, halted the roundup of Bundy's cattle and returned about 300 head to avoid any violence.
Authorities accused Bundy of conspiracy to commit an offense against the United States, assault on a federal law officer by use of a deadly and dangerous weapon, interference with commerce by extortion and obstruction of justice.
The indictment released on Wednesday said the eldest Bundy was the leader of the movement to extort the federal government into returning his cattle.
"The defendants recruited, organized, and led hundreds of other followers in using armed force against law enforcement officers in order to thwart the seizure and removal of Cliven Bundy's cattle from federal public lands," the indictment said. "Bundy had trespassed on the public lands for over 20 years, refusing to obtain the legally-required permits or pay the required fees to keep and graze his cattle on the land."
Bundy, 69, could spend the rest of his life in prison if convicted.
Arrested as he came to aid of sons
Cliven Bundy was arrested last week in Portland, where he flew in support of his sons Ammon and Ryan, who both allegedly participated in another, more recent armed standoff against federal authorities at the Malheur National Wildlife Refuge's headquarters in Harney County, Oregon.
That 41-day standoff ended last week after the last of the holdouts surrendered to authorities.
Ammon Edward Bundy, 40, of Emmett, Idaho, and his brother Ryan C. Bundy, 43, of Bunkerville, Nevada, are among 16 people indicted in the Oregon standoff, and each of the 16 defendants face a federal felony count of conspiracy to impede officers of the United States from discharging their official duties through the use of force, intimidation or threats, the FBI said.
The 16 defendants were described by the FBI as being among "dozens of highly armed militants occupying, visiting and supplying the refuge."
'Lawless and violent'
In arguing against bail for Bundy, federal prosecutors portrayed Bundy as "a danger to the community," according to court documents.
"Bundy is lawless and violent. He does not recognize federal courts -- claiming they are illegitimate -- does not recognize federal law, refuses to obey federal court orders, has already used force and violence against federal law enforcement officers while they were enforcing federal court orders, nearly causing catastrophic loss of life or injury to others," federal prosecutors said in court papers filed Tuesday.
Bundy lives on 160 acres as a long-time resident of Bunkerville, Nevada, a sparsely populated area near the borders with Utah and Arizona, court papers said.
The Bundy Ranch is near the Virgin River a few miles from where Interstate Highway 15 crosses into Arizona, or about 90 miles northeast of Las Vegas, authorities said.
Why it took almost two years for charges
In 2014, at the time of his alleged crimes, more than 1,000 head strayed as far as 50 miles from his ranch and into the Lake Mead National Recreational Area, "getting stuck in mud, wandering onto golf courses, straying onto the freeway (causing accidents on occasion)," authorities said in documents.
He allows his cattle to "run wild on the public lands with little, if any, human interaction until such time he traps them and hauls them off to be sold or slaughtered for his own consumption," prosecutors said.
In his April 2014 confrontation with federal authorities, "Bundy organized and led over 400 followers to assault BLM officers as they guarded the impoundment site, all for the purpose of getting cattle back," prosecutors said.
"In the immediate aftermath of the April 12 assault, federal law enforcement officers were forced to abandon the impoundment site, precluding them from conducting an immediate investigation," prosecutors said.
Out of safety concerns, local law officers allowed the gunmen and the conspirators to leave the site without facing arrest.
It took nearly took two years for authorities to finally file charges against Bundy because, prosecutors indicated, "the investigation became purely historical in nature."
"The presence of many gunmen in and near the area of Bundy Ranch, the armed checkpoints and patrols, the presence of assault weapons in the militia camps, including (by some accounts) a .50 caliber machine gun, further increased the difficulty of conducting a physical investigation of Bundy Ranch or the impoundment site," prosecutors added.