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Barnes & Noble’s first and only retail bookstore in the Bronx opened in December 1999. Credit Emon Hassan for The New York Times
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Update: Barnes & Noble executives said on Thursday that its store in the Bay Plaza in Co-op City will remain open for at least two more years.

The book lovers’ lament has been heard time and again in Manhattan. This time it is in the Bronx.

Barnes & Noble’s first and only retail bookstore in the Bronx opened in December 1999 after a relentless pursuit by the borough’s avid readers, but now plans to close at the end of the year, leaving the Bronx again without a major full-service bookstore to call its own.

A company executive said the chain decided not to renew its lease at the store in Bay Plaza in Co-op City after “exhaustive conversations” with the landlord, Prestige Properties & Development.

The store, which includes a cafe, has become an informal reading room and gathering spot for many Bronx residents, some of whom travel by buses and trains to get there. A custom-made mural above the magazine racks pays tribute to the borough with vintage postcards of Bronx landmarks, including Yankee Stadium, Fordham University, the Bronx River and Van Cortlandt House.

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Kenneth Pineda, 23, is a frequent patron of the bookstore, which is set to close at the end of the year. Credit Emon Hassan for The New York Times

The planned closing comes as the Bronx, once shunned by many developers, has seen an economic resurgence that has brought concerns of rising rents and gentrification to some neighborhoods. The borough is adding new retail and shopping complexes, boutique hotels and even a Donald Trump-branded golf course. In August, a three-story indoor shopping center, the Mall at Bay Plaza, opened in Co-op City just across from the Barnes & Noble.

The Barnes & Noble executive, David Deason, who is vice president for real estate, said that during discussions to renew the store’s lease, which expires in January, the landlord had communicated that it was able to lease the space to others in excess of what the bookseller paid.

Stephen B. Kaufman, who was a state assemblyman from the Bronx in the 1990s, said he led the three-year community effort to bring Barnes & Noble to the borough after he tired of traveling to Manhattan or Westchester County for his books. Barnes & Noble mostly ignored the entreaties, he recalled, until he and other organizers took their campaign public with petitions that garnered thousands of signatures and contentious news conferences in which they called the chain “Barnes & Ignoble.”

That effort got the attention of Leonard Riggio, then the chairman and chief executive officer of the bookseller, who wrote to Mr. Kaufman in February 1998, asking: “Do you have some sort of misplaced crusader complex which needs fixing? I mean, do you really believe that trashing people in public is a noble pursuit? Do you think that this Bronx-born native New Yorker needs you to tell him how great the Bronx is? Just wondering!”

Barnes & Noble executives said that Mr. Riggio was not involved in the decision to open the Bronx store or in real estate matters, and that the store was developed after a thorough evaluation. Mr. Kaufman attended the opening festivities the following year. (Barnes & Noble declined to give sales figures for the store.)

Now the bookstore that has meant so much to so many people in the Bronx plans to close at the end of December. The borough has a handful of specialized shops selling college textbooks, comics, and religious and Spanish-language books, but no other big general-interest bookstore.

“Where am I going to get my books now?” asked Carmen Poyer, 55, a retired social worker, as she left the store on a recent afternoon, clutching a copy of the novel “Gone Girl.” “I like to go in and look around. I like to feel the book, turn the page. I guess I’m old-fashioned.”

Velveeta Verdejo, 48, said that her son, Giovanni, 30, headed for the bookstore whenever he felt like trolling for comics and fantasy books, or just escaping from their apartment for a while. “I always know where to find my son when he’s mad at me,” she said.

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Stephen B. Kaufman was a state assemblyman in the 1990s who helped bring Barnes & Noble to the borough in 1999. On its plans to close, he said, “It’s like someone put a hand in your body and yanked out some of your heart.” Credit Richard Perry/The New York Times

Barnes & Noble, which has faced competition from online retailers and changing reading habits, is the last major national bookstore chain remaining after Borders closed in 2011. In recent years, Barnes & Noble has also closed stores at Lincoln Center and Astor Place in Manhattan after being unable to come to agreements with the property owners, Mr. Deason said. He added that the chain had sought to extend the leases and operations of those stores.

Barnes & Noble currently operates 658 stores nationally, including six in Manhattan, three in Queens, two in Brooklyn, and one each in the Bronx and on Staten Island. Mr. Deason added that there were no plans to reopen the Bronx store but that as the chain looked to open more stores, potential sites in the borough would be considered.

Maranda Ashkar, director of marketing for Prestige Properties & Development, the landlord for Bay Plaza and the Mall at Bay Plaza, said that Barnes & Noble’s option to renew its existing lease called for a rent increase based on a previous agreement. The company does not disclose rents, she said.

Once Barnes & Noble decided not to renew, Ms. Ashkar said, Prestige Properties tried to work with the bookseller by offering to let it stay at its current site month to month at a reduced rent until another long-term tenant could be found (with ample notice given to vacate). Prestige’s leasing agent, Welco Realty Inc., had also suggested a smaller space inside the Mall at Bay Plaza, and Barnes & Noble’s real estate agent declined, she said.

Mr. Deason said that the retail industry was seasonal, and that most retailers structured leases to expire in the period just after the year-end holidays, when store inventories would be low.

Mr. Kaufman, now a lawyer in private practice, said he had been fielding calls from Bronx residents who were upset about the closing. “It’s like someone put a hand in your body and yanked out some of your heart,” he said. “It hurts because this is a symbol of the intellectual coming-of-age of the borough and it’s just being removed because of a dispute between Prestige Properties and Barnes & Noble.”

But Mr. Kaufman and other Bronx leaders said they had not given up hope. A spokesman for Ruben Diaz Jr., the Bronx borough president, said that Mr. Diaz and his staff were working to negotiate a compromise between Barnes & Noble and Prestige Properties.

Marlene Cintron, president of the Bronx Overall Economic Development Corporation, said she would look into incentives to encourage Barnes & Noble to keep its store open, or to bring another bookseller to the Bronx. “This is a setback for me,” said Ms. Cintron, who goes to the Co-op City store once a month for her “book fix.” “Certainly the Bronx needs and deserves a full-service bookstore.”

For some Bronx residents, it will be hard to go back to a time when they did not have a bookstore nearby. Kenneth Pineda, 23, a Niketown sales associate who used to go to the Barnes & Noble with his parents, now takes his daughter, Kylie, 5, nearly every Sunday to pick out books for her growing collection.

“It’s really taking a lot away from here,” Mr. Pineda said. “There are always people reading books and drinking coffee in the cafe. I even see kids from school doing their homework. There are not many places like this anymore.”

Correction: October 22, 2014

An earlier version of this article misstated the number of Barnes & Noble stores in Queens. There are three, not one.