The 45-year-old, who was living in exile in the Chinese territory of Macau, was poisoned with the lethal nerve agent VX in a brazen Cold War-style assassination on February 13 in Kuala Lumpur International Airport.
Seoul has blamed Pyongyang for his death, but the North has rejected those claims and has never confirmed the identity of the victim, who was carrying a passport bearing the name of Kim Chol when he was attacked.
Deputy Prime Minister Ahmad Zahid Hamidi today revealed that the sample was "taken from the son... Who is living abroad".
Ahmad Zahid told reporters that Malaysian officials travelled overseas to an undisclosed location to collect the DNA sample.
"The DNA was taken and brought to Malaysia and matching was made and we confirmed that the body belonged to Kim Jong- Nam."
Two women - one Vietnamese and one Indonesian - have been arrested and charged with the murder. Airport CCTV footage shows them approaching the victim and apparently smearing his face with a piece of cloth.
The police chief has said he believes they fled to Pyongyang while the other three are hiding in North Korea's embassy in Kuala Lumpur.
Pyongyang has denounced the investigation as an attempt to smear the secretive regime, insisting that Kim most likely died of a heart attack.
The killing has triggered a bitter row between Malaysia and North Korea, which have expelled each other's ambassadors and barred their citizens from leaving.
In what may be the first comments by the family since Kim's death, a young man identifying himself as Han-Sol appeared in a video that circulated last week. The claim was later verified by South Korea's intelligence agency.
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