Jeffs is the brother of Warren Jeffs, the church's former President and convicted felon now serving a life sentence.
Jeffs was stopped as drove through the marina after using a bathroom, said Yankton County Chief Deputy Sheriff Michael Rothschadl.
His brother, Warren, 60, was displayed on a similar poster and captured nearly a decade earlier.
Jeffs' group, known as the Fundamentalist Church of Jesus Christ of Latter Day Saints, is based in a small community on the Utah-Arizona border.
Authorities have been looking for Jeffs since last June, when he escaped from home confinement in Salt Lake City.
Jeffs was granted release from jail last June despite Utah prosecutors arguing he'd be a flight risk.
The FLDS has a compound in Pringle, South Dakota.
Warren Jeff's former mansion in Utah is being bought by the 65th of his 79 wives, Brielle Decker, who has said she hopes to make it a tourist attraction and home for people who have left the church. Authorities overheard Warren Jeffs say on a recorded call from prison that Lyle should be "sent away", according to the Los Angeles Times.
Lyle Jeffs, a leader of the Fundamentalist Church of Jesus Christ of Latter Day Saints (FLDS), went on the run after the Federal Bureau of Investigation charged him and 10 other members of his sect previous year with food stamp fraud of at least $12 million and conspiracy to commit money laundering.
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But it was the alleged food stamp fraud that brought criminal charges - not just for Lyle Jeffs, but for almost a dozen church leaders and members. Members of the sect believe polygamy brings exaltation in heaven. Known to the faithful as "R23", the compound sits along a gravel road, secluded by tall pine trees, a privacy fence and a guard tower. "They dropped everything. A colleague in need, which was us, needed assistance, and they dropped everything that they did and without their assistance, we would not have had a successful conclusion", said Barnhart.
"This indictment is not about religion; this indictment is about fraud", U.S. Attorney John W. Huber said at the time. He was being held without bond on a Federal Marshals Service hold in South Dakota's Minnehaha County, according to booking records.
Prosecutors accused Mr Jeffs and other sect leaders of instructing followers to buy items with their food stamp cards and give them to a church warehouse where leaders decided how to distribute products to followers. He says he provided officers with store video and pawn paperwork. The money was then diverted to front companies and used to pay thousands for a tractor, truck and other items, prosecutors have said.
The defendants denied wrongdoing and said they were sharing food as part of their communal living practices.
Brenda Nicholson, who group up in Short Creek ( the combined towns of Hildale and Colorado City), and was able to escape, told Lake Powell Communications this morning, "I hope they keep him for a very long time".
Nine of them accepted plea deals and one had his charges dismissed.
Federal prosecutors will be under pressure from critics of the sect who believe federal prosecutors went too easy on the other defendants.
Sam Brower, the author and private investigator whose book "Prophet's Prey" helped to bring down Warren Jeffs, also communicated with Lake Powell Communications today. "They feel God protected them". If Jeffs had tried to forcibly remove the tracker in a different way, authorities would have been alerted more quickly.