"The second black box was found at 12:10 p.m. Moscow time," a source in the Russian Emergencies Ministry told RIA Novosti.
FlyDubai Boeing 737-800 plane coming from Dubai crashed at about 03:50 Moscow time (00:50 GMT) on Saturday while attempting landing amid poor weather conditions at the Rostov-on-Don Airport (ROV).
"The second flight data recorder of the crashed airliner has been found. Its condition is being currently evaluated in cooperation with experts," Russian Investigative Committee spokesman Vladimir Markin confirmed.
He added that the two flight recorders would be handed to the specialists for analysis and deciphering of the recorded data.
Investigators earlier found the crashed plane's first flight data recorder and its first voice recorder.
The Investigative Committee presented three versions of the cause of the tragedy: a technical fault, severe weather conditions and human error.