"The exercises are aimed at practicing interoperability of naval task forces, naval infantry units, naval aviation, and coastal artillery," the ministry said in a statement.
"The drills involve military personnel with experience of combat action during the special anti-terrorism operation in the east of the country," the statement said.
The reunification of Crimea was followed by the beginning of an armed conflict between Kiev and independence militias in eastern Ukraine. The West accuses Russia of fueling the fighting.
NATO has been boosting its military presence in Eastern Europe and the Black Sea since spring 2014, citing security concerns over alleged Russian aggression. Moscow has said that the NATO buildup could only further escalate tensions.