He was the young boy whose frail shoulders carried the future of Imperial Russia until Bolshevik revolutionaries murdered him and the rest of the Royal Family almost 90 years ago.

Now archaeologists are convinced that they have found the remains of Crown Prince Alexei, Tsar Nicholas II’s haemophiliac son and heir, and one of his four sisters, the Grand Duchess Maria. The discovery near the Urals city of Ekaterinburg, where the family was killed by firing squad, may settle an enduring controversy over the fate of the Romanov dynasty after the Communists seized power in 1917.

More than 40 bone fragments, seven teeth, three bullets and part of a dress have been sent to forensic science experts for examination. They were uncovered after archaeologists identified the burial site from a 1934 report to local communist bosses by Yakov Yurovsky, the lead executioner.

Andrei Grigoryev, of the regional centre for the preservation of historical and cultural monuments, told The Times that his team had uncovered vital extra clues by examining original shorthand records of the document typed by two local secretaries. This had enabled them to narrow down the search for the grave of the missing family members, which was only 60 metres from the spot where bones said to belong to the Tsar, the Tsaritsa Alexandra and three of their daughters were recovered after the collapse of communism in 1991.

The remains of Alexei, 13, and Maria, 19, were not found, helping to fuel an enduring legend that some of the family survived the massacre on July 17, 1918, in the basement of a nobleman’s house in Ekaterinburg, 900 miles (1,450km) east of Moscow. The absence of any bodies during the communist era prompted hundreds of spurious claims from people claiming to be Romanovs.

Nicholas and his family were detained after his abdication in 1917 and sent to Ekaterinburg the next year. They were shot at dawn, along with the royal doctor and three servants, then loaded into a lorry and dumped in a mineshaft. Yurovsky’s account explains that nine of the eleven bodies were covered in sulphuric acid and reburied near a railway crossing. The other two were burnt and buried some distance away.

“It is most likely that this second burial place is linked to the first one,” Sergei Pogorelov, a historian with the Sverdlovsk regional administration, told reporters yesterday. “Everyone knows who they belong to.” Nikolai Nevolin, the head of Sverdlovsk’s medical examination bureau, said that the remains showed signs of heat damage.

If the identities of the Tsar’s children are confirmed, their discovery is certain to prompt a resurgence of interest in Russia’s imperial traditions, which has been encouraged by President Putin. The Tsar and the rest of his family were reburied amid considerable controversy in the imperial crypt at the St Peter and Paul Cathedral in St Petersburg in 1998, on the 80th anniversary of their murders.

The Orthodox Church rejected the authenticity of the remains despite DNA tests by a British expert, Peter Gill, that confirmed they were those of the Romanovs. Patriarch Alexiy II refused to attend the service, saying that it was an “incontrovertible fact” that the Bolshevik regime had destroyed the royal remains completely. The Church canonised Nicholas II and his family in 2000.

President Yeltsin did attend the reburial, urging Russians to mark the occasion with repentance for a “bloody century”. He had his own reasons to repent: Mr Yeltsin oversaw the demolition of the house in which the Royal Family was killed as the communist boss of Ekaterinburg in 1977, as the Kremlin worried that it could become a rallying point for monarchists.

The historian Eduard Radzinsky, a biographer of Nicholas II, said that proof that the remains were those of Alexei and Maria would confirm Yurovsky’s report and the authenticity of the bones in St Petersburg. “This then would mean the remains now kept at the Peter and Paul Fortress, which we shamefully buried as the grave of an unknown soldier, are definitely the remains of the murdered Romanovs,” he told Russian television.

The Romanov descendants are split over which branch of the family is linked most directly to the Tsar and responded cautiously to the news of the find. A spokesman for Grand Duchess Maria Vladimirovna, who does not recognise the remains in St Petersburg as those of the Tsar, said: “It is too early to speak about any results, especially given the sad experience of the ‘Ekaterinburg remains’ buried in the Peter and Paul cathedral.” Ivan Artsishevsky, representing other members of the family, told Ekho Moskvy radio that people should be “very careful about all these finds” until more evidence was presented.”

The Prosecutor-General’s office said that it had reopened a criminal inquiry into the murder of the Romanovs after the discovery.

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