Stephen Noon, chief strategist at pro-independence campaign Yes Scotland, questioned the SNP's future in the event it achieves its ultimate aim.
He said independence would solve the constitutional question while altering the fundamental dividing lines of Scottish politics.
"What of the party of independence?" he wrote.
"Will Scotland still want or need an SNP?"
The party last night denied it would disband if it was successful in 2014, saying the SNP would be campaigning for votes "now and in an independent Scotland".
A senior party source insisted Mr Noon was merely pointing out how different Scottish politics would be after independence.
But opposition parties accused him of "muddying the waters" in an attempt to make independence appear less risky to voters. Mr Noon's comments, in a newspaper article, will also be viewed as part of a movement to de-couple the SNP from the idea of independence.
Yes Scotland campaigners are aware that they need to broaden their appeal if they want to win in 2014.
Most opinion polls suggest they have the support of just one-third of voters, leaving them well short of a majority.
Some political observers also pointed out that while Mr Noon raised the possibility of the SNP disbanding, he also speculated the Nationalists could see their appeal among traditional Labour voters grow.
He suggested they could even enter into a coalition with Labour at Holyrood.
The Scottish Conservative deputy leader, Jackson Carlaw, said: "Let's not kid ourselves that Alex Salmond and the SNP would just fade away after the referendum vote in 2014, no matter the result.
"From saying they will keep the Queen and the pound to asserting we would still be British under separation, the SNP tactic is plain to see – they will do and say anything to curry favour with as many people as possible."
He added: "Talk of whether the SNP will exist or not is just muddying the waters and another diversionary tactic in a bid to make their separation dream sound more palatable."
Mr Noon, a former Scottish Government special adviser, said independence would create a "fresh start" for Scottish politics.
With the constitutional question answered, all of Scotland's political parties could be transformed, he suggested.
He predicted Scottish Labour would no longer suffer the loss of talented politicians to Westminster, potentially transforming its electoral chances.
He also speculated the Tories could finally shake off the legacy of Thatcher by becoming an entirely separate party from the one left in the remaining UK.
Mr Noon also used the article to suggest Labour voters might also cast their vote for the SNP in some elections.
He wrote: "In this new world, with the most significant dividing line in Scottish politics erased, independence-focused SNP-ers could safely choose to give one or even both their votes to Labour (or Green or LibDem), and Unionist Labouristas could happily give one or both votes to the SNP.
"While for some this thought will have them spluttering into their porridge, most of us will recognise this as a real opportunity for a fresh start for Scottish politics, and for Scotland."
Patricia Ferguson, Scottish Labour's constitutional spokeswoman, said: "Given this government has ground to a halt and seems out of ideas, and that most Scots reject their core policy of independence, many people will be asking: 'What is the point of the SNP now?'"
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