Geneticists, forensic experts and investigators have long been certain who these remains belonged to -- Alexei, the 13-year-old son of the last tsar Nicholas II, and his sister Maria, who were shot along with their family by the Bolsheviks in 1918.
But despite DNA evidence of their identity, objections from the country's powerful Orthodox Church mean the bones remain unburied almost a century after the brutal slaying.
Now a new probe is aiming to finally lay the controversy to rest -- and the remains too, next to the other members of Russia's last royal family, interred back in 1998 in their former capital Saint Petersburg.
The Church does not accept that any of the remains of the tsar's family are authentic and says it needs to make sure beyond doubt, as it has proclaimed all the family members saints and martyrs.
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Russia's government went ahead regardless with the other burials in 1998 but is now seeking to resolve the row with the Church before burying the others.
This summer, Russian Prime Minister Dmitry Medvedev renewed calls to lay Alexei and Maria to rest with their parents and sisters.
To satisfy them, investigators reopened the tombs of Nicholas II and his wife Alexandra, and are set to exhume Nicholas's father Alexander III.
The first results of the new tests are coming back once again confirming their identity and experts say they are struggling to see what further objections the Church could have.
But the Church is still hesitant to recognise the DNA evidence and argues that although it is willing to make the historic move, it must "rule out the possibility of any mistake whatsoever" and conduct its own research.