The Defense Ministry said the two Su-34 jets, each with a crew of two, collided while maneuvering and went down 35 kilometers (22 miles) from the shore.
It said both crews bailed out and one crewman was quickly spotted and rescued by a helicopter. He was in good condition, according to the ministry.
Following a massive search involving several rescue ships and aircraft, two other crewmen were found dead, the ministry said in a statement carried by Russian news agencies.
The search for the fourth missing pilot is continuing despite strong winds.
Earlier, the Defense Ministry said two crewmembers were rescued, but later retracted the report and said that just one crewman has been found alive.
The ministry said the jets were not carrying any weapons.