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The future King was called into action during the early hours of Sunday morning after the Swanland, a massive vessel loaded with 3,000 tonnes of limestone was buffeted by high winds.
William was on the mission, which lasted into the following day, for several hours.
On Sunday, another search and rescue chopper – not thought to have the Prince at the controls – left the RAF base to continue the search for the five men who remained stranded at sea.
Ray Carson, who is watch manager at Holyhead Coastguard, said the tragedy was the result of unsettled waters.
He said one of the rescued men described the ship being "hit by an enormous wave".
"It rolled the ship and broke its back. (The survivor) said this led to a catastrophic failure of the vessel."
William's role in the rescue operation earned him a letter of thanks from the Russian ambassador.
Alexander Yakovenko wrote: "We know that... the two seamen were saved thanks to your selfless effort under the bad weather conditions.
"Let me express to you and your colleagues my deepest gratitude for saving the lives of the Russian citizens."
Sunday's mission marks an important moment in William's career as an RAFpilot.
Early next year he will be deployed to the Falklands for a six-week rotation at the Mount Pleasant base.
The action man royal finished his search and rescue course in September 2010, after training extensively at the controls of Sea King helicopter.
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