Billy Brown and Jim Jefferies had been in charge at Rugby Park for eight years
Kilmarnock have parted company with manager Jim Jefferies and his assistant Billy Brown, saying the decision was made "by mutual consent".
The announcement comes days after a row broke out between striker Kevin Kyle and chairman Michael Johnston.
But Johnston told BBC Scotland: "It is totally unrelated.
"I am personally sad they have gone. Supporters were becoming frustrated and that maybe played a part in his decision reach this agreement."
Kyle had claimed that Johnston had asked him to discuss 59-year-old Jefferies' tactics and selections.
Johnston has denied those claims and has confirmed that the Killie captain faces disciplinary action.
They have a bunch of players who, if they get the breaks, will secure their Premier League status fairly comfortably and can finish in sixth or seventh
But the chairman refused to be drawn on that or the events that led to the departure of his management team, pointing out that there was a confidentiality agreement with Jefferies and Brown that restricted his comments.
Johnston had on Saturday voiced his support for the former Berwick Rangers, Falkirk, Hearts and Bradford City manager, who had consulted his lawyers over the Kyle row and whose eight-year reign at Rugby Park has now ended.
"Nothing has changed," Johnston said of the man who could now be linked with the managerial vacancies with Dundee United and Motherwell.
"I have always supported Jim Jefferies. I gave him a new contract not that long ago that would have seen him here until 2012.
"He would, by then, have been the longest-serving manager we have ever had and that would have been a fitting accolade for someone with his long experience in Scottish football.
"He and Billy are the longest-serving management team in Scottish football and have vast knowledge of the Scottish Premier League in particular and all the players in it and I'm sure they will do a great job wherever they end up."
The future remains uncertain for Kyle, the 28-year-old Scotland striker who is out of contract in May.
"There will be disciplinary action taken against Kevin Kyle, but that's an internal matter for the club," said the chairman.
"Part of the problem that we have had in recent months is that too much of the club's business has been getting into the media.
"We need to put a stop to that, so I'm not going to go into Kevin Kyle's disciplinary proceedings."
Kilmarnock, heavily in debt, have slipped to second bottom of the SPL after winning just one of their last nine games, but Johnston said they would not be rushing the appointment of a new manager.
The chairman said that former Killie defender Alan Robertson would have a major role to play in any interim arrangement.
However, the problem for Johnston, who described Saturday's league match against Motherwell and next week's Scottish Cup tie against Falkirk as vital for the club, is that Killie's youth coach is presently in Turkey with the under-19 squad.
Jefferies' relationship with Johnston had deteriorated in recent months as Kilmarnock grappled with the cost-cutting required by the loss of the SPL's broadcasting deal with Setanta.
Kilmarnock had withdrawn an offer of a coaching job to former player Gary Locke in the summer.
That did not go down with the players, who were also unhappy at a new disciplinary system imposed by Johnston, while team captain Kyle recently went public with his concerns about Killie's lack of a club doctor.
However, Jefferies confined his comments to praising the players he left behind.
"I enjoyed my eight years at Kilmarnock," said the former manager, who took the squad for training on Monday.
"They have a bunch of players who, if they get the breaks, will secure their Premier League status fairly comfortably and can finish in sixth or seventh."
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