Keith Alexander, who was in charge when Irish businessman MacAnthony acquired the club, left in January 2007.
After managing to retain the services of Aaron Mclean, Craig Mackail-Smith and George Boyd in the summer, Johnson brought in a host of fresh faces to bolster his squad.
But despite strength in attack Posh have looked fragile in defence, shipping 42 goals in their 21 league games this season.
And after a 3-0 home defeat by Brighton in October and a 5-1 reverse to Charlton in November the pressure started to build.
Posh lost 6-2 to Fulham in the FA Cup on Saturday but they are undefeated in their last four league outings and it would seem disagreements with MacAthony, rather than form, have cost the ex-Cambridge United chief his job.
Former Peterborough United winger Tommy Robson told BBC Radio Cambridgeshire he was sad to see Johnson go.
"We've had so many managers in so short a time, it's one league we're top of I think," Posh's all time record appearance holder joked.
"Gary's a great lad, he's welcoming and his teams have always played well.
"He's has some bad luck at the minute, obviously George Boyd's injured and he's a key player, so things haven't been rosy for the lad all the way through."
Posh have named youth-team boss David Oldfield as caretaker manager.
Peterborough thrash Walsall in Johnson's last league match
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