The Ultimate Bagel Company, popular with undergraduates since it opened in Harvard Square more than three years ago, will close its doors forever today.

Ultimate Bagel--known among students for its toaster oven, low prices and fresh coffee--is one of only two stores in the Square specializing in bagels, with Mount Auburn Street's Bruegger's Bagel Bakery being the other.

A source close to the company said today's closing is the result of high rent charged by Harvard, which owns the property.

The source would not disclose the amount the company pays in monthly rent, but said the Harvard Square location is the only branch currently having financial problems.

Scott Levitan, director of University and Commercial Properties, which manages the property, said he is negotiating a new lease with a local business that will open there in February, after some renovations to the site.

Toscanini's, Inc., an ice cream manufacturer, appears likely to fill the location, said its owner, Gus Rancatore, who confirmed that his company is negotiating with the University to lease the property.

Ultimate Bagel, which has two other locations in Massachusetts besides its Harvard Square location, will open another store in Stoneham in about six months, the source close to the company said.

The closing of the store should provide a financial boost to Bruegger's, which is now in place to corner the market for local bagel sales.

"It will definitely help, because I know they do somewhat of a good business," said Bruce G. Kihanya, the supervisor on duty at Bruegger's last night.

And although ice cream vendors in the Square acknowledged that a new Toscanini's would be an unfortunate source of competition, they said they are not worried that their businesses will be hurt.

Herrell's Ice Cream on Dunster Street has outlived several other ice cream parlors that were in the Square when it opened 14 years ago, according to Jessica G. Leahy, its owner and manager.

"We've got a really great, loyal following of customers," she said. "I think there's plenty of market share around for everybody."

No Layoffs

A sign on the door of Ultimate Bagel yesterday announced that all of its employees will be transferred to other locations and will not lose their jobs.

Lily B. Perry, who was making bagel sandwiches for the seven customers who crowded the small store yesterday afternoon, confirmed that the sign was correct. She added that she will begin working at the Newbury Street location in Boston after the Harvard Square site closes.