The Scots-born presenter of the BBC's flagship Sunday morning political discussion programme, The Andrew Marr Show, told a packed audience at the Edinburgh International Book Festival he was concerned about the tone of the debate after seeing opponents denounce each other as traitors.
Marr, who recently suffered a stroke, warned the run-up to next year's referendum could provide a platform for a deeply entrenched Anglophobia he claimed lay behind attacks directed at United Kingdom Independence Party (Ukip) leader Nigel Farage during a recent visit to Edinburgh.
The SNP said it was disappointed by Marr's comments.
The Glasgow-born former BBC political editor was in the city to promote an updated version of his 1992 book, The Battle For Scotland.
On clashes between the rival pro- independence and pro-UK campaigners he said: "It's getting very aggressive.
"I would posit that, whatever your view, there is no-one here who is a traitor.
"There is nobody who deserves to be denounced, cast out and told they are not really Scottish on the basis of their view.
"Whatever happens, you are all going to have to live together."
He noted that the Ukip leader was treated to a rough time when he was heckled and told to go back to England by pro-independence and self-styled anti-bigotry campaigners.
He said: "Now, as I understand it, whatever you think of him, Nigel Farage is trying to get independence for Britain from Brussels, which is not necessarily totally different from trying to get independence for Scotland from London.
"But your neighbour's nationalism is always toxic and xenophobic and your nationalism is always good."
He added: "There is a very strong anti-English feeling [in Scotland]. Everybody knows it, there always has been.
"If you go back to the origins of the SNP, the origins of home rule, Anglophobia was as well-entrenched then as it is now.
"I don't think it is particularly serious most of the time, but it can become serious, it can become toxic."
Marr said Alex Salmond was a political genius who had a plan for next year's referendum campaign and should not be written off.
Dismissing claims by US polling guru Nate Silver that the Nationalists stood no chance of winning the referendum, he insisted the result would be much closer than the polls suggest and there was still a lot to play for.
Marr said he would choose a Scottish passport over a British one if the country became independent.
He said the rest of the UK had failed to consider the consequences of Scottish independence which, he claimed, could include the loss of the country's nuclear deterrent and its seat on the UN Security Council, the dilution of its voting power in the EU and a re-ordering of domestic politics.
Marr, who was aided by a walking stick, revealed he was still unable to type following his stroke.
An SNP spokesman said: "We are happy to see that Andrew Marr's health is recovering, but we are disappointed by the picture of Scotland he has painted in his reported comments.
"It is simply wrong to suggest that aspirations for Scotland to make our own decisions are based on anything other than a desire to build a fairer, more prosperous Scotland.
"Intolerance of any kind has no place in Scotland and all of us have a duty to stand up to it where it occurs."