The 10,000-square kilometre site contains hydrothermal vents that could yield metals including gold, silver, copper, zinc and lead, the maritime ministry said in a statement.
The general assembly of the International Seabed Authority last Friday voted to give Seoul the exclusive right to develop the area -- around 2,500 kilometres southwest of Sri Lanka -- from 2013 to 2027, it said.
The ministry estimated production would reach about 46,000 tonnes, worth $320 million, a year.
"This is the result of aggressive efforts by the government and related agencies on investment, research and international diplomacy... amid fierce global competition to secure resources," it said.
Hydrothermal vents are areas on the ocean floor where water heated by volcanic activity under the seabed gushes out.
Seoul officials and scientists explored the area from 2009 to 2011.
The resource-scarce South has strengthened efforts in recent years to secure raw materials overseas. Including the new mine, it has the right to develop four deep-sea mines totalling 112,000 square kilometres.