Earlier in the morning, the South Korean military spotted a small boat carrying the two in the waters north of Baengnyeong Island near the western inter-Korean sea border.
The two, of whom one is a soldier, told the military that they were willing to defect to South Korea, Yonhap news agency reported.
It is the first defection since April, when the leaders of the two Koreas held a summit and reached an agreement on a wide range of measures to ease tensions and pursue various economic cooperation projects.