The stunning news, which has been confirmed by the Defence Ministry, the Navy and the U.S. firm leading the search for the vessel, arrived in the early hours of Saturday morning. Relatives of the crew still have questions. "Now we are going to search for the truth".
According to a tweet from the Argentine navy, the ARA San Juan had been positively identified under the water by a U.S. company.
Argentina's government bowed to pressure from the families of the missing crew in January by offering $US4.8 million ($A6.5 million) for information leading to the submarine's recovery.
Ocean Infinity used five autonomous underwater vehicles to carry out the search, according to a statement from the company.
Families of the crew say they are determined to fight for the rescue of the submarine and those inside.
"Much of what happens from here will have to be resolved by the justice department", Aguad said.
Relatives gathered to remember their loved ones earlier this week, while President Mauricio Macri promised to keep up the search for the submarine.
The San Juan, a German-built TR-1700 class submarine, vanished nearly exactly one year ago as it was sailing from the southernmost port of Ushuaia to Mar del Plata after a patrol.
The navy said previously the captain reported on November 15, 2017, that water entered the snorkel and caused one of the sub's batteries to short-circuit.
Teams will dive down to whatever is left of the San Juan during an operation that is expected to last about seven hours, but defence minister Oscar Aguad has warned that the country "does not have the means to recover the wreckage".
The German-built diesel-electric TR-1700 class submarine dated back to the mid-1980s and had been most recently refurbished in 2014, when it was cut in half as its engines and batteries were replaced. Naval commander Gabriel Galeazzi said the ship surfaced and its crew explained they had a "short circuit" in the vessel's batteries.
Over a dozen global partners including the United States helped the Argentine Navy search for the ARA San Juan for weeks, though the search was stymied by rough weather and was eventually called off it became increasingly unlikely that any crew could have survived.