After family notification, Rexburg Police said they found two sets of unidentified human remains.
The children, Tylee Ryan, 17, and Joshua Vallow, whose eighth birthday was on May 23, vanished sometime previous year.
Investigators say Daybell and Vallow allegedly lied about the children's whereabouts and left for Hawaii.
It's another grim turn in a case that drew global attention with its ties to the couple's doomsday beliefs and the mysterious deaths of their former spouses.
Law enforcement officers first searched Chad Daybell's home on January 3 in connection with Tammy's death, removing more than 40 items including several pieces of computer equipment. The family reportedly declined an autopsy before her burial in Utah.
Vallow's ex-husband also died under suspicious circumstances shortly before her marriage to Daybell.
A booking photo of Chad Daybell, who was arrested Tuesday. At the time, Cox said the shooting was in self-defense. She's in jail on $1 million bond. The Idaho attorney general's office announced this year that it was investigating Chad Daybell in the death of his wife at the time, Tammy Daybell. Cox died in December, and a medical examiner's office in Arizona recently declared this a "natural" death, though the Gilbert Police Department said at the time in May that they were still investigating.
Authorities learned that Tylee was last seen alive on September 8, in Yellowstone National Park, prompting the FBI to ask anyone who visited the park that day to come forward with photos and videos, which can be uploaded to FBI.gov/Rexburg.
The National Center for Missing and Exploited Children describe Joshua Vallow, age 8, as white, with brown hair, and brown eyes. Results of an autopsy in that case have not yet been released.
Meanwhile, JJ's grandparents, Larry and Kay Woodcock of Louisiana, were growing increasingly anxious about the kids.
Chillingly, wherever Vallow and Daybell were, people turned up dead. Eventually, a judge ordered Lori Daybell to prove the children were safe by bringing them to officials.
She was living there with Daybell when the children's grandparents asked local police to perform a wellness check. They watched JJ's birthday arrive in late May.
Vallow was arrested in Hawaii in connection with her children's disappearance on February 20 and was extradited back to Idaho. "Our Rexburg family hosted a poignant vigil on Monday 5/25 in honor of our little man".
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