Assistant Rexburg Police Chief Gary Hagen told reporters that Daybell was being questioned after a search warrant was served on his home. He said detectives had recovered unidentified human remains in their investigation of the missing children.
Hagen did not provide additional details about the warrant, which was sealed. Media were not allowed near the home during the search.
Police confirmed to NBC affiliate KTVB of Boise that the search warrant was related to the disappearance of JJ Vallow and Tylee Ryan, who were 7 and 17 years old respectively when they disappeared in September.
In a December statement, police said that Vallow and Daybell were refusing to cooperate with the investigation into the missing children, which began in November, and that they had left the state.
After Vallow and her husband were found in Hawaii, she was arrested in February and extradited to Idaho on charges of desertion and nonsupport of dependent children. She is being held on a $1 million bond.
Vallow has pleaded not guilty, according to The Associated Press.
Vallow is also being investigated in the death of her husband's former wife, Tammy Daybell. The body of Daybell, 49, was found in her home in October, a death initially ruled as natural but since classified as suspicious.
In December, her remains were exhumed for an autopsy, the results of which are pending, according to KTVB.
Chad Daybell, a self-published author who has written more than two dozen books about near-death and doomsday events, and Vallow married weeks after Tammy Daybell's death. They have not been charged in that case.
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Vallow's fourth husband, Charles Vallow, also died last year. He was shot to death in July by Vallow's brother, Alex Cox, during a confrontation.
Vallow and Cox were questioned by police but not charged. Cox died in December.