The former SNP leader made the announcement on her Instagram on Monday morning.
In a post headed “personal”, Sturgeon wrote: “With a heavy heart I am confirming that Peter and I have decided to end our marriage.
“To all intents and purposes we have been separated for some time now and feel it is time to bring others up to speed with where we are.
“It goes without saying that we still care deeply for each other, and always will.
“We will be making no further comment.”
The news comes after Murrell was charged in connection with embezzlement amid an ongoing police investigation into the SNP’s finances, dubbed Operation Branchform.
Murrell, who was the SNP’s chief executive from 2001 to 2023, was charged by police in April 2024.
Sturgeon has also been arrested and questioned by police investigation the SNP, but was released without charge in June 2023.
Earlier this month, leading Scottish defence KC Thomas Leonard Ross predicted that the state of play meant that Sturgeon would not be charged amid the Operation Branchform probe.