The jury sent a note to the judge indicating it had reached an impasse in the trial of Warren Jeffs, president of the Fundamentalist Church of Jesus Christ of Latter Day Saints. Jeffs is charged with two counts of rape as an accomplice.
"We have a hung jury regarding the second count," the jury said in a note. "We do not believe further deliberation is needed. How do we go about it at this point?"
The judge advised them to look at their instructions and keep talking.
Jurors planned to work into the evening, court spokeswoman Nancy Volmer said.
The young woman in the case testified that she pleaded with church leaders to hold off the marriage because of her age but was told her "heart was in the wrong place." She said she sobbed through the ceremony and had to be coaxed to say "I do" and kiss her groom.
The groom, Allen Steed, however, said the young bride initiated sex within weeks of the ceremony. He insisted he never forced her to do anything.
The Associated Press generally does not identify people alleging sexual abuse.
Each count of rape by accomplice against Jeffs represents a time frame in the marriage. The first count covers April 23, 2001 - the day of their wedding - to May 12, 2001. The second count covers May 13, 2001, to Sept. 30, 2003.
Jeffs, 51, has led the FLDS church since 2002. Followers see him as a prophet who communicates with God and holds dominion over their salvation; ex-church members say he reigns with an iron fist, demanding perfect obedience from followers.
Jeffs was a fugitive for nearly two years and was on the FBI's Most Wanted list when he was arrested during a traffic stop outside Las Vegas in August 2006. If convicted, he could spend the rest of his life in prison.
Jeffs is not charged with being a polygamist, and the three-year marriage between the cousins was monogamous. Still, polygamy casts a shadow over the case.
Polygamy advocates have long contended that the freedom to practice plural marriage as part of their religion is a civil rights matter. Members of FLDS, which broke away from the Mormon church, believe polygamy brings exaltation in heaven.
The Mormon church disavowed polygamy in 1890 and excommunicates members found to be practicing plural marriage.