Two men -- in their 20s and 50s -- swam across the Yellow Sea border to the South's island of Gyodongdo at 4:00 am (1900 GMT Wednesday), Yonhap news agency said, citing a Seoul government official.
They were spotted by marines and expressed a desire to defect, Yonhap quoted the anonymous official as saying.
Seoul's defence ministry spokesman was not immediately available for comment.
The duo are expected to be interrogated by Seoul's intelligence authorities before being sent to a resettlement centre for defectors.
The heavily-fortified island is about 2.5 kilometres (1.55 miles) away from the closest North Korean shore.
It is extremely rare for defectors to try and swim over the border, although it was not immediately clear just how far the two men had come.
Last month, a North Korean man sailed across the Yellow Sea border in a boat.
Most North Koreans who flee repression and poverty at home cross the porous border with China first before travelling to a Southeast Asian nation and eventually arriving in the South.
Few defect across the heavily-fortified land border between two Koreas marked by barbed wires and guarded by tens of thousands of troops on both sides.