In a statement on Saturday, the Rexburg Police Department said the bodies of 17-year-old Tylee Ryan and 7-year-old Joshua Vallow, known as JJ, had been officially identified.
Mr Daybell is married to the mother of the deceased, Lori Vallow, and the official identification of the remains is the latest grim turn in a case that began with the disappearance of the two children in late 2019.
"It is not the outcome we had hoped; to be able to find the children safe. Our hearts and prayers go out to the families of JJ and Tylee," the police statement said.
Mr Daybell was taken into police custody on Tuesday after the discovery of the bodies at his rural Idaho property. He is being held on $1m bond.
A prosecutor said then that they belonged to the children and the way one was concealed was “particularly egregious”. He did not elaborate.
Global media attention was drawn to the case due to Chad Daybell and Lori Vallow Daybell’s doomsday beliefs and the suspicious deaths of their former spouses.
The couple married in September 2019, a few weeks after authorities say her children were last seen.
Having lied to investigators about the children’s whereabouts they quietly left Idaho for Hawaii, where they were found several months later.
Ms Vallow Daybell was arrested in February in Kauai. She has been charged with child abandonment and obstructing the investigation. She is in jail on $1m bond and intends to defend herself against the charges.
The complex case began with Ms Vallow Daybell’s brother shooting and killing her estranged husband, Charles Vallow, in suburban Phoenix last summer in what he asserted was self-defence.
Mr Vallow was seeking a divorce, saying his wife believed she had become a god-like figure who was responsible for ushering in the biblical end times.
Her brother, Alex Cox, died in December of an apparent blood clot in his lung.
Shortly after Mr Vallow’s death, Lori and the children moved to Idaho, where Chad Daybell lived.
Mr Daybell ran a small publishing company, putting out many fiction books he wrote about apocalyptic scenarios loosely based on the theology of The Church of Jesus Christ of Latter-day Saints. He also recorded podcasts about preparing for biblical end times, and friends said he claimed to be able to receive visions from “beyond the veil.”
He was married to Tammy Daybell, who died in her sleep last October of what her obituary said were natural causes.
Authorities became suspicious when Mr Daybell and Ms Vallow married just two weeks later.
Tammy Daybell’s body was exhumed in December, but the results of the subsequent autopsy have not been released.
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