The boat was spotted in the Yellow Sea, the body of water that lies between South Korea and China. Aboard the vessel were a civilian and a major in the North Korean military.
"They expressed the willingness to defect," the source said.
The defection came days after North Korea declined to allow South Korean journalists to observe the closure of its nuclear test site, which occurred on Friday. It has been less than a month since the historic summit between the two Koreas, where North Korea's Kim Jong Un met with South Korean President Moon Jae-In.
Read more: From Little Rocket Man to denuclearization: A timeline of US-North Korea relations under Kim Jong Un
Uncommon defectorsThe last defection by a North Korean military officer took place in 2008, according to Korean broadcaster YTN TV. Saturday's defection was the 14th involving a North Korean soldier since 2000.
Last November, a North Korean soldier drove into the heavily guarded border at speed and ran across under a shower of gunfire from his own side.
Another North Korean soldier walked unchecked across the border in 2012, avoiding rows of electrified fencing and surveillance cameras. Three field commanders were sacked as a result.
More than 30,000 North Korean civilians have fled the country. However, it is very rare for them to cross the Korean border, which is fortified with minefields and barbed wire.
Most flee across the Yellow Sea into neighboring China.
dv/sms (AFP, Reuters)