The frigate Admiral Essen and submarine Krasnodar carried out four strikes against military hardware and fighters from the jihadist group who had left its de-facto capital Raqa, the Russian military said in a statement.
"All the targets were hit," the statement said, without specifying when the strikes happened.
Moscow said that the US, Turkish and Israeli military "were informed in a timely manner of the missile launches through existing communication channels."
President Vladimir Putin was briefed on the successful strikes by Defence Minister Sergei Shoigu, the Kremlin said.
Russia has been conducting a bombing campaign since 2015 in support of President Bashar al-Assad and has a naval contingent deployed to the eastern Mediterranean to bolster its firepower.
Moscow has, however, not announced any strikes from the sea in recent months as it focuses on pushing a fragile truce between the government and rebels.
Islamic State is not included in the ceasefire.
