"The main black box was found at 5:42 am Moscow time (0812 IST) 1,600 metres from the shore at a depth of 17 metres," the defence ministry said in a statement, adding that the device would be sent to the Moscow region to be deciphered by experts.
The Tu-154 jet, whose passengers included more than 60 members of the internationally renowned Red Army Choir, was heading to Russia's military airbase in Syria when it went down off the coast of the resort city of Sochi shortly after take-off on Sunday.
The finding of the black box comes as searchers are scrambling to recover bodies and remaining debris from the aircraft in an operation involving 192 divers, 45 vessels, 12 planes, five helicopters and 15 deepwater machines.
The defence ministry said that five plane fragments were found overnight 30 metres under water at around 1,700 metres from the shore.
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Part of the plane's fuselage, measuring 3.5 metres by 4.5 metres, was recovered yesterday evening.
The defence ministry said today that 12 bodies and 156 body fragments had been recovered from the water since the crash. They will be sent to Moscow for identification, it said.
The Kommersant daily newspaper reported that investigators are relying on a witness statement by a coast guard member who saw the plane in its final moments descending toward the sea with its nose tilted sharply upward.
Authorities have not said how long it would take to decipher the black box, which could provide information on the reasons for the crash.
The FSB said all passengers remained on the plane when it stopped in Sochi, with one customs officer and one border guard coming on board as it was being fuelled.
Onboard were 64 members of the Alexandrov Ensemble - the army's official musical group, also known as the Red Army Choir - and their conductor Valery Khalilov. The choir was set to perform for Russian troops at the Hmeimim airbase in Syria, which has been used to launch air strikes in support of Moscow's ally President Bashar al-Assad.