Mr MacAskill and wife Alison had been married for 22 years before separating earlier this year. It is believed the couple fought to save the marriage for several months after encountering problems in 2008.
But it emerged yesterday that Mr MacAskill had moved out of the family home in Edinburgh and into a one-bedroom flat.
The politician confirmed he had spilt with Alison – the mother of his two sons, aged 22 and 20 – in a short statement, adding that they remained "good friends".
Mr MacAskill, the MSP for Edinburgh East and Musselburgh said: "My wife and I separated on the best of terms after some months trying to reconcile, and no third party has ever been involved."
According to reports, friends of the couple believe his high-pressure job may have played a part in the separation in May.
The past year has seen Mr MacAskill face many difficult and high-profile situations, putting him at the forefront of Scottish politics.
Last October, Lockerbie bomber Abdelbaset Ali Mohmed al-Megrahi was revealed to be suffering "advanced stage" prostate cancer, prompting calls from Libya for him to be released from his life sentence.
In March this year, Libya's minister for Europe Abdulati Alobidi met with the Scottish Government to discuss the case. Then, in April, a prisoner transfer agreement (PTA) between the UK and Libya came into force, allowing Megrahi to apply to serve the rest of his sentence in a Libyan jail.
In May, the Scottish Government revealed Libyan authorities had applied for the transfer of Megrahi – around the same time Mr MacAskill and his wife separated.
And in August, Mr MacAskill announced his decision to return Megrahi to Libya on compassionate grounds, amid growing criticism from around the world.
Mr MacAskill has also been under pressure over Scotland's open prisons after a series of escapes by inmates.
In 2007, Robert Foye absconded from Castle Huntly for the second time while serving a ten-year sentence for attempted murder.
In May this year, murderer John Brown went on the run from Castle Huntly days after another prisoner, Brian Martin – nicknamed The Hawk – handed himself into police after escaping the same jail.
Professor Cary Cooper, a psychologist at Lancaster University, said:
"People in the public eye do have a lot of pressure on them and it can affect their relationships."
He added: "Being a politician is not like most jobs. You work long hours and are not with your family as much.
"On top of that, it can be very stressed. Mixed together, it can have a serious effect on your life away from work."
HIGH-PROFILE CASES THAT PUT MINISTER IN THE SPOTLIGHT
THE pressure heaped on Kenny MacAskill over the Lockerbie bomber was undoubtedly the most intense of his career.
However, earlier this year, there was speculation that a vote of no confidence in the justice secretary would be brought to Holyrood after the escape of dangerous prisoner Brian Martin, nicknamed "The Hawk", from Castle Huntly jail in Perthshire.
In March 2008, Mr MacAskill offered a public apology after a 16-year-old girl was raped by Robert Foye after he too had absconded from Castle Huntly.
And the justice secretary sparked a furious backlash last May after describing prison as a "bit of a skoosh" for short-term prisoners.
Mr MacAskill's critics have also accused him of presiding over a "soft-touch" justice system after it emerged some people convicted of attempted murder and serious assault had been given prison sentences of less than six months. Opponents have also seized on a 30 per cent rise in community service orders for criminals.
The number of such orders issued by courts rose from 4,298 in 2003-4 to 5,593 in 2007-8.
Mr MacAskill has also faced heavy criticism over his plans for minimum pricing of alcohol.