"There is likely, at least, another felony charge that will come because of his conduct over the last year," Huber said.
During a morning news conference in Salt Lake City, FBI Special Agent in Charge Eric Barnhart said Jeffs, who was living out of a newer Ford F-150, was arrested near a marina in Yankton, S.D.
The FBI and local police began scouring the town Tuesday after receiving a tip from the public, Barnhart said.
The owner of a Yankton pawnshop says Lyle Jeffs revealed whom he was on Tuesday when he pawned two pairs of Leatherman pliers for $37 and provided identification, according to The Associated Press.
River City Treasures and Pawn owner Kevin Haug says a store employee notified him that Jeffs was wanted by the FBI after Jeffs had left the store.
Haug says Jeffs provided his last name as his first name, going by Jeffs Lyle Steed.
Haug then read about Jeffs on the internet and called Yankton police. He says he provided officers with store video and pawn papers, the AP reported.
Haug says Jeffs also visited the store last week and tried to sell a tool but the store did not buy it that time and Jeffs did not identify himself during the earlier visit.
He says Jeffs during his first visit was fidgeting, seemed nervous and "acting like a freak," according to the AP.
Yankton County Chief Deputy Sheriff Michael Rothschadl says authorities looked for Jeffs in the area because of the tip from the pawnshop, which included that Jeffs had left in a silver pickup, possibly with Utah plates.
Authorities were looking for the vehicle and an off-duty police detective spotted it Wednesday night at the Lewis & Clark Marina, according to Rothschadl.
He said the detective saw Jeffs go into a restroom at the marina and then drive away after exiting. Yankton police made a traffic stop, and Jeffs was taken into custody without incident, Rothschadl said. The sheriff's office, South Dakota Highway Patrol and the FBI assisted in the arrest.
The FLDS has a compound in South Dakota, though it is on the opposite side of the state — about 425 miles away from Yankton.
Barnhart declined to give details about the tipster or whether the person had an association with the FLDS, but said, "It's a great story."
Jeffs spent the night in the Minnehaha County jail in Sioux Falls. He was being held without bond.
"When you flee a federal indictment, the long arm of the law will eventually catch up with you and bring you to justice," Huber said, adding that Jeffs' flight from justice will play a part in his upcoming prosecution in the food stamp case.
While the FBI believed Jeffs was removed from his position as bishop while evading law enforcement, FLDS member Norma Richter on Thursday expressed support for the man many FLDS members still call "Uncle Lyle," and doubted the government's accusations.
"I have no reason to believe anything other than he's honorable and the whole case against him was foolish," she said.
"There was really no case," Richter added. "So I don't know why they were still chasing him."
Jeffs and the other defendants were arrested in February 2016 as part of a federal raid on FLDS offices and two businesses. Each was charged with one count each of felony conspiring to defraud Supplemental Nutrition Assistance Program (SNAP) and felony conspiracy to commit money laundering for allegedly diverting millions of dollars' worth of their benefits.
Prosecutors allege FLDS leaders required sect members to turn over to the church their SNAP cards or the food purchased with them, and in some cases SNAP benefits were used at church-controlled stores and converted to cash.
Federal prosecutors and the FBI fought hard to keep him in jail pending trial, but Jeffs' attorneys persuaded U.S. District Judge Ted Stewart to set him free with monitoring.
Huber said Thursday: "You don't want to say, 'I told you so,' but that's kind of where we're at."
He added that he doesn't anticipate that Jeffs will be eligible again for pretrial release or house arrest.
Jeffs appeared to use olive oil to slip off his GPS ankle monitor and abscond from home confinement in Salt Lake County late June 18 or early June 19, according to the FBI.
Meanwhile, Jeffs' co-defendants, including his full brother and another FLDS bishop, Seth Jeffs, resolved their cases by pleading guilty to felony or misdemeanor charges.
Representatives of the FBI and the U.S. attorney's office in Utah have said no such offers will be made to Lyle Jeffs.
Huber said the team that prosecuted the fraud case "eagerly awaits" Lyle Jeffs' day in court. "We do not discuss plea negotiations, if there are any," Huber said Thursday. "That being said, we have always viewed Mr. Jeffs as the lead defendant in this prosecution."
Defense attorney Aric Cramer, who represented co-defendant Kristal Dutson, on Thursday said it is unlikely prosecutors have a stronger case against Lyle Jeffs than they did against the co-defendants. While prosecutors see the case as using the SNAP to divert food and cash to FLDS leaders, Cramer said that parishioners were following their beliefs and consecrating their government benefits to their church.
"I don't think they're going to get much more out of him than they did against [Seth Jeffs]," Cramer said. "They're kind of in the same position."
Lyle Jeffs is a younger, full brother to imprisoned FLDS President Warren Jeffs. At the time of his arrest, Lyle Jeffs was the bishop of Short Creek — an area comprised of Hildale, Utah, and adjoining Colorado City, Ariz. — and the person in charge of day-to-day operations of the FLDS. After the arrests, FBI documents filed with the courts show, Warren Jeffs reassigned the bishop duties to another brother, Nephi Jeffs.
The FBI had offered a reward of up to $50,000 for Lyle Jeffs, but otherwise the search for him had been much lower key than the hunt for Warren Jeffs in 2006. The older brother, who at the time was facing charges of rape as an accomplice in Utah, was placed on the FBI's list of Ten Most Wanted Fugitives.
Former FLDS members expected Lyle Jeffs to evade law enforcement much the same way Warren did — with prepaid cellphones and a network of dwellings across the West that the FLDS call "Houses of Hiding." But the FBI in August described a rift between Lyle and Warren Jeffs and said there was evidence Lyle had been hiding in Short Creek.
The FBI hoped that lessened status within the sect would limit the help he received from church members. Barnhart said Thursday the early indications were that those hopes came to fruition.
"His level of support and his means of continuing that flight was limited," Barnhart said.
Barnhart said it is believed Lyle Jeffs had been in the Yankton area for two weeks. The FBI will investigate where he has been and who, if anybody, aided him, Barnhart said.
The FBI pledged a similar investigation after Warren Jeffs was captured in 2006 near Las Vegas. Another brother, Isaac Jeffs, and one of Warren Jeffs' wives also were in the vehicle stopped on Interstate 15. However, neither they nor the owner of the Cadillac Escalade was ever charged with a crime for helping the fugitive.
At the time of his arrest, Warren Jeffs was charged in Utah with being an accomplice to rape. The Utah Supreme Court overturned that conviction, but Warren Jeffs was convicted later in Texas of charges relating to sexually abusing two girls he married as plural wives. He is serving a sentence of life in prison plus 20 years.
Lyle Jeffs' legal wife divorced him in 2015, but family members say he still has eight spiritual wives.
— Reporter Jessica Miller contributed to this story.
Editor's note: An earlier version of this story included an erroneous detail about penalties for Lyle Jeffs' co-defendants.