- 5 updates
Wendi Deng gained popularity for springing to her husband's aid when a protester threw a custard pie at him as he appeared before MPs to answer questions about phone hacking in 2011.
At 44, Ms Deng is 38 years younger than Mr Murdoch, who is 82.
Rupert Murdoch's divorce filing said the "relationship between husband and wife has broken down irretrievably," according to a New York Times report.
It added that a spokeswoman for News Corporation, his media company, confirmed that it was Mr Murdoch who had made the filing.
The spokeswoman added that the divorce would have no impact on the company.
Rupert Murdoch's first marriage to flight attendant Patricia Booker took place in 1956 and lasted 11 years. They had one daughter, Prudence, in 1958.
In 1967, he married the Scottish-born journalist Anna Torv after the pair met at his Sydney-based newspaper The Daily Telegraph.
They had three children together - Elisabeth, Lachlan and James - over the course of more than 30 years of marriage.
Within a month of their divorce in 1999, Murdoch married Chinese-born TV executive Wendi Deng with whom he had two more daughters - Grace and Chloe.
Wendi Deng is perhaps best known in Britain for defending husband Rupert during a physical attack at a parliamentary hearing in 2011.
The Chinese-born businesswoman was seen landing a slap on the face of activist Johnnie Marbles, who had attempted to throw a foam pie at Mr Murdoch.
News Corporation chief executive Rupert Murdoch has filed for divorce from his wife Wendi, the company confirmed.
Murdoch, 82, married Wendi Deng, his third wife, in 1999. The reasons for the filing were not immediately clear.