Borders Group Inc.'s decision to liquidate promises to be a headache for landlords throughout the country, but some will be worse off than others.

A location near the New York Stock Exchange in lower Manhattan is likely to get filled soon, said Gene Spiegelman, the Cushman & Wakefield broker representing the landlord. It was one of the 200 stores that Borders announced in February that it was planning to close.

But at the other end of the spectrum is Agree Realty Corp. ADC +0.33% Agree Realty Corp. U.S.: NYSE $30.48 +0.10 +0.33% April 8, 2014 4:06 pm Volume (Delayed 15m) : 52,604 AFTER HOURS $30.48 0.00 0.00% April 8, 2014 4:30 pm Volume (Delayed 15m): 8,201 P/E Ratio 21.29 Market Cap $454.61 Million Dividend Yield 5.64% Rev. per Employee $3,053,180 More quote details and news » , a small real-estate investment trust based in Farmington Hills, Mich. Borders is Agree's third-largest tenant and provides 9% of its annual rental income, according to research firm Janney Capital Markets

Many of Agree's properties are in markets where it still is difficult to find tenants. Andrew DiZio, an analyst at Janney Capital, predicts that Agree will give up about five properties to lenders. "I expect a voluntary default on those mortgages," he said in an interview Tuesday.

Agree Realty officials couldn't be reached. But in a regulatory filing this year, the company said it was in default on three properties secured by Borders.

Borders' liquidation announcement means that it will close another 399 stores on top of the roughly 200 closings announced earlier this year, when it filed for bankruptcy protection.

Mall and shopping center owners said they have been planning for this worst-case scenario. Some already have initiated discussions with possible replacement tenants and are considering plans to break up floor space that will be vacated by the Borders stores to make it easier for a new tenant or repurpose it for mixed use.

For the malls and retail properties in secondary or weak markets, finding new tenants could be more of a feat as big retailers like Best Buy Co., which were rapidly expanding, are backing away from the big-box format and are opting for smaller stores.

"Demand for space of that size may be limited," said Cedrik Lachance, an analyst at research firm Green Street Advisors.

Borders' largest landlords include Westfield Group WDC.AU +0.14% Westfield Group Australia: Sydney $10.49 +0.01 +0.14% April 9, 2014 1:49 pm Volume : 2.27M P/E Ratio 14.25 Market Cap $21.74 Billion Dividend Yield 4.86% Rev. per Employee N/A 02/26/14 Australia's Westfield Group co... More quote details and news » and General Growth Properties Inc., GGP +0.04% General Growth Properties Inc. U.S.: NYSE $22.30 +0.01 +0.04% April 8, 2014 4:01 pm Volume (Delayed 15m) : 5.03M AFTER HOURS $22.30 0.00 0.00% April 8, 2014 4:30 pm Volume (Delayed 15m): P/E Ratio 79.30 Market Cap $19.70 Billion Dividend Yield 2.69% Rev. per Employee $1,731,130 03/24/14 What's the Deal From the Wall ... 03/18/14 Plots & Ploys 02/24/14 Same-Day Delivery Startup Deli... More quote details and news » said Mr. Lachance. Given that many of their Borders are located in high-performing malls, the two companies may have a less difficult time filling the space as opposed to Pennsylvania Real Estate Investment Trust, PEI +0.61% Pennsylvania Real Estate Investment Trust U.S.: NYSE $18.17 +0.11 +0.61% April 8, 2014 4:01 pm Volume (Delayed 15m) : 306,048 AFTER HOURS $18.17 0.00 0.00% April 8, 2014 4:30 pm Volume (Delayed 15m): P/E Ratio N/A Market Cap $1.24 Billion Dividend Yield 4.40% Rev. per Employee $701,275 More quote details and news » which operates malls in weaker markets.

Alan Barocas, head of leasing for General Growth, said Tuesday that the mall landlord already has found new tenants for some stores, but declined to give specifics.

"We have been actively marketing them in anticipation of these locations coming back to us. That's not to say we will re-lease all of them soon, but we're pretty comfortable mitigating our risk on this," he said.

Mr. Barocas said one benefit is that many of those leases were signed about seven years ago at below-market rents. "We have the ability to replace tenants at rents that were above Borders'," he said.

Some landlords said they have been planning for Borders' liquidation. Above, a store in New York City. Bloomberg News

Joseph Coradino, head of services at Pennsylvania REIT, said the mall company has leasing deals in the works for most of their soon-to-be-vacant stores, which are mostly in smaller locations. The company plans to break up a superstore in Newport, Va., into a restaurant and several stores.

Mr. Coradino said the company already has re-leased several spaces with local and regional book retailers.