A leading investigator involved in the probe, Vladimir Solovyov, told the Echo of Moscow radio station that they had taken "samples from Nicholas II, from the empress, and from the uniform of emperor Alexander II," the last czar's grandfather, who was himself assassinated in 1881.
"We have decided to start again from the very beginning and carry out renewed examinations," said Solovyov. The remains will be subject to genetic testing, he added.
The powerful Investigative Committee confirmed some of the family's remains were being re-examined, with spokesman Vladimir Markin saying the probe would look into "the circumstances of the death and burial of the imperial family."
The czar, his wife, their five children and their servants were shot by the Bolsheviks and thrown into a mineshaft in 1918 before being burnt and hastily buried.
Russia first looked into the murder of the family after a mass grave was discovered in 1991 near Yekaterinburg in the Urals, where the royal couple and their five children were exiled and shot after the Russian Revolution.
Scientists said that DNA evidence was sufficient to conclude that the grave contained the remains of the czar and czarina, along with three of their daughters, and the government officially identified them in 1998.
The remains were then re-buried in the erstwhile imperial capital Saint Petersburg.
In 2007, a second grave was discovered at a different spot containing two more bodies, believed to be those of the czar's heir Alexei and daughter Maria, who were 13 and 19 years old when they were killed.
But their remains have since been stored at the Russian State Archives, amid doubts over their identity.
While Russian criminal investigators ruled in 2008 that the remains of Alexei and Maria were authentic after DNA testing, their identity has not been accepted neither by the Russian Orthodox Church, which has canonized the last Romanovs, nor by some Romanov descendants.
In July, the resurgent Russian Orthodox Church pressed for the case to reopened.
The question of the authenticity of the remains has taken on fresh urgency ahead of the looming centenary of the murder, as Russia wants to bury all seven family members together.
Read more at Discovery News
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