Warren Jeffs considered a "prophet" by his followers was wanted for alleged sexual misconduct with minors in Arizona and as an accomplice to rape in Utah. He is being held in a county jail awaiting extradition to either Utah or Arizona.
He is accused of arranging marriages between older men and underage girls in his sect, which is generally closed to outsiders.
Young men and boys are often forced out to ensure a supply of young brides for male elders.
The 50 year old was stopped by the Nevada Highway Patrol because of expired license plates on his vehicle.
When the patrolman recognized Jeffs he held him at the scene until FBI agents could arrive and positively identify him.
The FBI had offered a 100,000-dollar reward for information leading to his arrest.
Sect leader
Jeffs was travelling with one of his wives and a brother at the time of the arrest, which occurred about 10 kilometres north of Las Vegas. He had been on the run for at least two years.
Special Agent David Nanz said Jeffs had a "large sum of cash, several wigs and various communication radios."
"He was taken into custody without incident," said Lieutenant Steve Cabrales of the Nevada Highway Patrol.
Jeffs assumed control of his sect, known as the Fundamentalist Church of Jesus Christ of Latter-day Saints, also called the Fundamentalist Latter Day Saints, or FLDS, from his now-deceased father when the elder leader suffered a debilitating stroke in 1998.
The sect is based in an enclave on the twin border towns of Hildale, Utah, and Colorado City, Arizona and is believed to be one of the largest polygamist sects that exist in the United States.
It split from the Church of Jesus Christ of Latter-day Saints when the mainstream Mormon Church banned polygamy more than a century ago.