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The sample was obtained by Malaysian authorities who went overseas to get it, Malaysia Deputy Prime Minister Ahmad Zahid Hamidi said.
Kim Jong Nam was killed February 13 in what Malaysian Prime Minister Najib Razak has called an assassination attempt. Kim was at Kuala Lumpur International Airport on his way to Macau when two women wiped his face with the highly lethal VX nerve agent, killing him in 20 minutes, Malaysian police said.
He declined to elaborate on how the DNA sample was obtained.
It's not clear when the video was shot, but a South Korean National Intelligence Service spokesman verified the son's identity to CNN.
The row over the body
The decision to hold Kim Jong Nam's body -- and conduct an autopsy -- angered the North Koreans. They wanted the body and said Malaysia should hand it over because he was a North Korean national.
Nine Malaysians are in North Korea. It's not clear how many North Koreans are in Malaysia, but police believe three people wanted for questioning in Kim's killing are holed up in the North Korean Embassy in Kuala Lumpur.
There are four suspects at large, believed to be back in North Korea, and two people in custody regarding the case.
Red notices are described by the US Justice Department as the "closest instrument to an international arrest warrant in use today." But they only pertain to countries that are INTERPOL members, which North Korea is not.
Siti Aisyah of Indonesia and Doan Thi Huong of Vietnam have both been charged with murder and face the death penalty if convicted.
Authorities from both countries have said the women believed they were participating in a prank TV show, but Malaysian authorities do not believe that's true.
CNN's Joshua Berlinger reported and wrote from Hong Kong, while journalist Salhan K. Ahmad reported from Kuala Lumpur. CNN's Marc Lourdes contributed to this report.