The Armavia airline Airbus A-320 disappeared from the radar and crashed off the coast shortly before it was to land in the Russian city of Sochi - a popular holiday resort town.
Invesigators have blamed stormy weather conditions for downing the plane, which had been making a short flight from the Armenian capital, Yerevan.
"According to preliminary information, all people on board are dead," a ministry spokeswoman said.
Around 30 bodies have been pulled from the water, emergency officials said.
None was wearing a life jacket, indicating they did not have time to prepare for an emergency landing.
In Sochi's airport, about 100 tearful relatives - nearly all Armenians - kept up an anguished vigil in a waiting hall.
Gurgen Seroboyan, whose 23-year-old fiancee Lucenie Gevorkian was a flight attendant on the plane, wept as he waited at Yerevan airport for a charter flight that was to take relatives of the crash victims to Sochi.
"We were planning to get married and then this tragedy happened," he said.
Relatives of those on board
gathered at Sochi airport
Vladimir Putin, the Russian president, and his Armenian counterpart Robert Kocharian declared Friday a day of mourning in both countries.
Beltsov said the plane vanished from radar screens on Wednesday as it was approaching Adler airport near Sochi, a Russian resort near the Georgian border, at 2:15am (2215 GMT).
Viktor Beltsov, the Russian emergency situations ministry spokesman, said that the wreckage from the plane, which crashed early on Wednesday, was found not far from the shoreline.
Baggage, body parts, pieces of the shattered plane and oil floating on the Black Sea were also found at the site of the crash, the emergencies ministry said.
A deep-sea robot was also being used to try and locate the plane's black box recorder, the emergency ministry added.