Kevin Pringle, the First Minister's most trusted lieutenant, stepped down as a special adviser within the civil service.
He takes up a new post as the SNP's director of strategic communication, based at the party's headquarters in Edinburgh, on September 10.
He will work closely with SNP deputy leader Nicola Sturgeon, supporting her role as the party's representative on the board of the cross-party pro-independence Yes Scotland campaign.
Mr Salmond's aide Geoff Aberdein has been promoted to chief of staff, co-ordinating the work of the SNP's team of special advisers. The three start in their new roles on Monday as MSPs prepare to return to Holyrood after their summer break.
Mr Salmond paid tribute to Mr Pringle, 44. He said: "Kevin has given more than five years of outstanding service as a special adviser to the SNP Government, and is returning to the party where he played a key role in the SNP's election victory in 2007 and landslide re-election last year.
"I'm delighted his talents will now be deployed in helping deliver a Yes vote in the independence referendum."
Mr Pringle said: "It has been a huge privilege to work for the first ever SNP Government – which was resoundingly re-elected on the basis of our positive record, team and vision for Scotland. And it will be an even greater privilege to play a part in achieving a Yes vote."
Insiders insisted that Mr Salmond was executing a long term plan to put his most skilled media operator into one of his party's most important jobs.
He would have struggled to install him as communications director at the Yes Scotland campaign without alienating prospective cross-party allies, such as the Scottish Greens.
Scots LibDem leader Willie Rennie said the move was evidence of tensions at the top of the SNP Government, following reported Cabinet-level disagreements over whether to pursue a one or two-question referendum strategy.
Mr Rennie said: "The departure of such a senior figure shows all is not well within the nationalist camp. This is an admission the SNP has lost momentum and is losing the debate on Scotland's future."
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