Wanderers fans have been urged to stay in their seats -- or parts of the Reebok Stadium will be closed.
Safety officials -- who fear lives could be in danger by fans flouting the no standing order -- have warned the Premiership club they will shut down large sections of the ground.
Today a Wanderers spokesman said: "Please help us so that we can continue to enjoy supporting Bolton Wanderers in safety without it affecting your privileges at the ground."
The closure threat comes after hundreds of fans stood up for much of the 4-0 home defeat by Manchester United. Town hall safety chiefs, who have the power to temporarily close parts of the ground, have made it clear they will not tolerate similar behaviour in the future.
They say the Football Licensing Authority could refuse to licence part of the 27,8000 capacity ground if they think there is a risk.
A letter to the club from Bolton Council safety experts warns, there was "mass persistent standing in both the lower and upper tiers of the South Stand, and a section of the South East corner. This went on for the virtually the full 90 minutes."
A spokesman for Bolton Wanderers said today: "It would be a huge disappointment to the fans and the club if the popular South East coroner had to be closed.
But some Wanderers fans feel said the closure threat is an "over-reaction". Lifelong Wanderers fan Gary Parkinson, aged 27, said: "The United game will always be a passionate game and people will stand up.The United fans were standing up and the feeling was: 'If they are, why shouldn't we?' Persistent standing needs to be dealt with by the stewards in a more friendly manner."
The move follows identical threats made by Trafford Council to Manchester United. But no action has been taken.
Bolton Council said the problem had been gradually building up all season and there was particular concern that fans had been standing on the upper tier, which was even more serious.
The club now has to put an action plan in place at the Reebok stadium.
Another fan Simon Maddrell, aged 36, from Smithills, but who now lives in London, is a lifelong fan who goes to all the away games and most home games.
He added: "To turn round the week after the United match and put the onus on Bolton fans is somewhat galling."
"I experience the behaviour of Bolton fans at home and away and it's not a major problem at all. They should be writing to Manchester United."
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