Tsar Nickolas II, his wife, their four daughters and son, and several servants, were shot dead by the Bolsheviks in a basement in the Urals city of Yekaterinburg in the early hours of July 17, 1918. The Romanovs were canonized in 2000.
Russia's Investigation Committee marked the anniversary by confirming Wednesday that the bone fragments exhumed near Yekaterinburg last July belong to the emperor's son and heir, and one of his four daughters.
"The overall data obtained during a DNA analysis ... supports the theory that the remains of Crown Prince Alexei and Grand Princess Maria have been found," the committee said referring to DNA and other tests carried out in Russia, the United States, and other countries.
The remains of Nicholas II, his wife Empress Alexandra and three daughters were found in Yekaterinburg in 1991 and reburied in 1998 in St. Petersburg, the Russian imperial capital.
The last tsar's great-grandson, Dmitry Romanov, who heads the Romanovs for Russia foundation, welcomed the news. "It is very important to me. It is an official confirmation... The family had hoped this would happen some day."
However, the Russian Orthodox Church, which has doubted the accuracy of similar tests 10 years ago, urged more studies to prove that the remains belong to the tsar's children.
The Russian church leader, Patriarch Alexy II, said Tuesday that "the 1918 atrocity" gave a start to a string of tragic events in Russia in the 20th century - "the horrors of war, fratricidal conflicts, famine, and unprecedented political repressions."
The patriarch also called on the government to condemn the killing of the emperor and his family, an appeal the Communist leader described as "provocative" and "an attempt to rewrite history."
The Russian Imperial House in exile has sought since 2005 to have the Romanov family exonerated as victims of political repression. Grand Duchess Maria Romanov, who heads the House, insists the killings were a state-sponsored execution rather than murder.
Russia's judiciary has rejected the demands saying the Romanovs never faced any formal charges before being executed by Bolsheviks.