Kirsten Farage said the ex-Ukip leader had moved out of the family home in Kent and that the situation “suited everyone”.
Her comments followed newspaper reports Mr Farage was sharing a house in west London with the French director of a think-tank.
Mr and Mrs Farage wed in 1999. In a statement on LBC, Mr Farage said: “Can I just add a personal comment. Some of you will have seen press coverage over the last few days and no doubt there’ll be more of it.
“About a few personal difficulties that I’ve had with my marriage and my family and my relationships.
“But I make this please, particularly to the media, please leave my wife and children alone – don’t hassle them, don’t initiate them. They don’t deserve it and it’s simply not fair.”
Nigel Farage has pleaded for his family to be left alone by the media
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In a statement to the Press Association Mrs Farage, who was born in Germany, said: “My husband I have lived seperate lives for some years and he moved out of the family home a while ago.
“This is a situation that suits everyone and is not news to any of the people involved.”
On Monday Mr Farage tore into the Speaker of the House of Commons John Bercow and said he had insulted President Donald Trump.
Mr Bercow said the President should not be allowed to address Parliament during his state visit.
Mr Bercow's extraordinary attack reignited controversy over the invitation to Mr Trump, provoking applause from MPs who oppose the US president, and drawing accusations the Speaker was "insulting" the UK's closest ally.
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Please leave my wife and children alone
The Speaker appeared to brand Mr Trump a "racist" as he said the president's travel ban on Muslims from seven countries, and refugees, had hardened his hostility to any high profile Westminster address during the visit.
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"I think the speaker of the House of Commons should be neutral. To have expressed political opinions in the way he did today devalues his great office, is insulting to President Trump," Nigel Farage told the BBC.
He continued his criticism on his own show on LBC, saying: “The Speaker of the mother of Parliament, one of the great institutions on the globe, commands respect by being neutral.
“What Bercow did today broke every single rule of that.
Nigel Farage in pictures Thu, December 15, 2016
Nigel Farage is a British politician who has been the leader of the UK Independence Party since October 2016.
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British politician Nigel Farage arrives at Trump Tower on December 15, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration.
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“His job is to not make political statements of that nature and I think in doing so he has devalued the office of Speaker, and that is a very sad thing indeed.”
The row erupted after Mr Bercow said addressing Parliament was "not an automatic right, it is an earned honour" for foreign leaders.
Labour leader Jeremy Corbyn backed the Speaker, tweeting: "Well said John Bercow. We must stand up for our country's values. Trump's state visit should not go ahead."
The Lord Speaker, Tory former Cabinet minister Lord Fowler, was not consulted by Mr Bercow and will make his own statement on the issue to peers on Tuesday.
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