By Robin Sidel 

American Express Co. said its 16-year-old exclusive relationship with warehouse club Costco Wholesale Corp. will end next year, dealing a blow to the card company that has already been falling short of its revenue goals.

The loss was unusually significant for the New York company, as Costco cards account for one out of every 10 AmEx cards in circulation and 20% of the company's loan portfolio. The move led Chief Executive Ken Chenault to hold a conference call with analysts to discuss the expected negative impact to the company's earnings for the coming two years, as well as its plans to counteract the loss.

AmEx, which issues credit and charge cards and owns a processing network, said it had been unable to reach a new agreement with Costco on terms that "would have made economic sense" for the company.

"It's not easy to see a long-standing partnership end, but when the numbers no longer add up it's the only sensible outcome," Mr. Chenault said in a conference call with analysts.

The news battered AmEx shares, which fell 6% to $80.82 in afternoon trading.

Co-branded Costco cards represent 8% of AmEx customers' world-wide spending, said Jeffrey Campbell, AmEx's chief financial officer. Another 1% of spending comes from other types of AmEx cards that are used at Costco, he said.

Costco had $110 billion in sales in its fiscal year that ended in August.

Costco is one of the few big U.S. merchants that only accepts AmEx cards. Credit cards branded by Visa Inc., MasterCard Inc. and Discover Financial Services can't be used at Costco warehouse stores. Costco, however, does accept debit cards from Visa and MasterCard.

AmEx said the pact would end on March 31, 2016. AmEx will discontinue its TrueEarnings cards that are branded with the Costco logo and offer new types of cards to those customers.

Customers who have other AmEx cards also won't be able to use them at Costco, which is expected to soon reach a new deal with another card company.

A spokesman for Costco declined to comment on its plans to replace the AmEx arrangement.

The end of the Costco relationship represents the latest setback for AmEx, which once was known as a status symbol for the affluent but is now under attack from competitors like J.P. Morgan Chase & Co. that are also going after wealthy Americans. AmEx is now trying to expand into other areas, such as pitching prepaid cards for low-end consumers and getting more small businesses to accept its cards. The strategy will likely take years to pay off.

Costco has long been one of AmEx's biggest partners. AmEx also has a big exclusive arrangement with Delta Air Lines Inc., which it renewed last month.

Such partnerships, called "co-brands," are established to build loyalty among specific types of customers. Cardholders often receive extra perks when they use co-branded cards, while card companies and the merchant typically see higher levels of spending on those cards.

AmEx's partnership with JetBlue Airways Corp. is also expected to end soon, but that is a far smaller relationship than Costco or Delta, according to a person familiar with the arrangements.

Mr. Chenault said the Costco pact's end would have a negative impact on revenue and earnings per share in 2015 and 2016. "We believe we have a number of different ways to drive growth going forward," he said, referring to the company's recent expansion into prepaid debit cards and other strategies.

AmEx will pursue efforts to convince the holders of the Costco branded cards to use other AmEx products. Mr. Chenault said that about 70% of spending on the Amex-Costco-branded cards is done in places other than at the warehouse club.

"They are AmEx customers as much as they are Costco customers," Mr. Chenault said.

Mr. Chenault said he is confident that the company will be able to achieve its earnings-per-share growth target of 12% to 15% in the "moderate to long term" without the Costco arrangement.

"We will invest in other opportunities that we think can generate greater returns over time," he said in the conference call.

Meanwhile, earnings per share are now expected to be "flat to modestly down" in 2015 compared with 2014 and then return to growth in 2016, Mr. Campbell said.

The dissolution of the partnership comes just a few months after AmEx and Costco ended their similar arrangement in Canada. Costco now has a partnership in Canada with MasterCard and Capital One Financial Corp.

Mr. Chenault said the end of the Costco deal could help raise AmEx's so-called discount rate, which is the amount that merchants pay for each transaction. Co-branded partnerships typically give the merchant a break on that rate as part of an incentive for doing the deal.

AmEx announced last month it was eliminating 4,000 jobs. The move came as part of an effort to control expenses amid a shortfall in revenue targets.

AmEx is awaiting a judge's verdict in a federal antitrust case that took place last summer. The Justice Department sued AmEx over its merchant rules, contending that they inhibit competition.

AmEx has said its policies aren't anticompetitive. It has also said it could suffer a "material adverse effect on our business" if it loses the case.

Write to Robin Sidel at robin.sidel@wsj.com

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