Choi Kye-wol broke down in tears when she was reunited with her son, Kim Young-nam at the Mount Kumgang Resort in North Korea.
Kim is thought to have been kidnapped by North Korean agents from an island off South Korea’s west coast in 1978.
He is believed to have married Megumi Yokota, a Japanese woman taken by North Korea.
South Korean pool video reports showed Kim with a teenage girl, who was said to be Hye-gyong, the daughter he is supposed to have had with Yokota. Kim also came with his new wife and a son by her, reports said.
In Japan, Yokota's mother, Sakie, told Reuters that she thought it was dangerous to go to North Korea, which might use the visit for propaganda, but she sympathised with Kim's mother.
On Wednesday, after viewing footage of the reunion, she told reporters, "I don't know what happened. I don't know the truth. But I'm just glad the mother and son were able to meet."
Yokota was 13 when North Korean agents kidnapped her in 1977. Pyongyang has said Yokota married a North Korean man in 1986 and gave birth to a daughter, who is now 18 and lives in the North. It also said Yokota committed suicide in 1994 while being treated for depression.
Tokyo says the resolution of the abductee issue is a condition for improving ties with Pyongyang. North Korea has admitted to abducting 13 Japanese in the 1970s and 1980s to help train its spies.
South Korea has opted for quiet diplomacy with the North in an attempt to gather information about more than 1,000 South Korean civilian abductees and Korean War prisoners believed to be living there.