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."
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.
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