A federal judge in Boston said Friday that American Airlines and JetBlue Airways must dismantle a partnership in the Northeast, an arrangement that allowed the carriers to coordinate operations on certain routes and share the profits.

The decision from U.S. District Judge Leo T. Sorokin is a victory for the Justice Department, which under President Biden has increased scrutiny of proposed deals in industries where it says there is too little competition to the detriment of consumers. Experts had said a favorable ruling for the two airlines could have led other carriers to form similar partnerships.

“Today’s decision is a win for Americans who rely on competition between airlines to travel affordably,” Attorney General Merrick Garland said in a statement. “The Justice Department will continue to protect competition and enforce our antitrust laws in the heavily consolidated airline industry and across every industry.”

In his 94-page decision, Sorokin noted that before forming their Northeast Alliance, JetBlue and American “vigorously competed on everything from fares to the features they offered customers.”

“The NEA changes all of that,” he wrote. “It makes the two airlines partners, each having a substantial interest in the success of their joint and individual efforts, instead of vigorous, arms-length rivals regularly challenging each other in the marketplace of competition. Though the defendants claim their bigger-is-better collaboration will benefit the flying public, they produced minimal objectively credible proof to support that claim.”

The loss is a setback for both carriers, particularly JetBlue, which is smaller than others in the market. Teaming with American enabled JetBlue to significantly expand its presence in the Northeast, where it had a small share of the market.

“The Court’s legal analysis is plainly incorrect and unprecedented for a joint venture like the Northeast Alliance,” American said in a statement. “There was no evidence in the record of any consumer harm from the partnership, and there is no legal basis for inferring harm simply from the fact of collaboration.”

Executives at JetBlue said they were disappointed by the decision.

“We made it clear at trial that the Northeast Alliance has been a huge win for customers,” JetBlue said in a statement. “Through the [Northeast Alliance], JetBlue has been able to significantly grow in constrained northeast airports, bringing the airline’s low fares and great service to more routes than would have been possible otherwise.”

Both carriers said they were considering their next steps.

Sorokin’s decision came two months after the Justice Department moved to block JetBlue’s attempt to merge with Spirit Airlines, saying the $3.8 billion deal would reduce competition and could lead to higher fares. DOJ attorneys said the loss of Spirit would be particularly harmful for price-sensitive consumers who depend on Spirit’s low fares.

American and JetBlue announced the creation of the Northeast Alliance in July 2020. The Department of Transportation gave the carriers approval to form the alliance in the waning days of the Trump administration as long as certain conditions were met. The DOJ challenged the agreement later in 2021, and the case was heard last fall in U.S. District Court in Massachusetts.

JetBlue and American argued that the partnership wasn’t a merger, but a limited arrangement that allows the carriers to better compete against Delta Air Lines and United Airlines, which dominate the New York-area and Boston markets. In court, they argued that the agreement has given consumers more flight options and available seats.

But the Justice Department, joined by attorneys general in Arizona, California, Florida, Massachusetts, Pennsylvania, Virginia and the District, argued that the arrangement was a de facto merger that harms consumers because it removes incentives for the carriers to compete in one of the nation’s busiest travel corridors.

While agreements such as the Northeast Alliance are rare among domestic carriers, they are common internationally. American Airlines is a founding partner of OneWorld, an alliance of international carriers that includes British Airways, Japan Airlines and others, sharing planes and airport space around the globe. The ruling Friday may close the door for similar arrangements domestically.

Diana Moss, president of the American Antitrust Institute, a nonprofit that seeks to promote competition, said the Northeast Alliance was different because the carriers didn’t just coordinate schedules, but also shared revenue.

“When you share revenue, you immediately eliminate the incentive to compete against each other, because if you did, it would be like robbing Peter to pay Paul,” she said.

Still, some airline analysts saw benefits in allowing American and JetBlue to join forces to compete against Delta and United. Kerry Tan, associate professor of economics at Loyola University Maryland, said that since the launch of the Northeast Alliance, American and JetBlue have continued to expand the number of cities they serve.

Henry Harteveldt, an aviation analyst and president of Atmosphere Research, said consumers will ultimately lose out. He said the alliance made it easier for JetBlue and American to coordinate on schedules, which in turn made it easier for people to travel.

“Frankly, the Department of Justice handed Delta Air Lines and United Airlines big victories, because while I expect that JetBlue and American will appeal this or at least try to appeal this ruling, if they’re unable to appeal or if their appeal is unsuccessful, it just means that Delta and United, which operate their own large hubs at Kennedy Airport and Newark Liberty International Airport, respectively, will not face the same level of competition.”

Even so, Sorokin viewed the alliance between the two carriers differently.

“The question before the Court is whether the NEA suppresses or promotes competition,” he wrote. “The record supports only one answer. The NEA, operating as it was designed and intended by American and JetBlue, substantially diminishes competition in the domestic market for air travel.”

Assistant Attorney General Jonathan Kanter, who leads the Justice Department’s antitrust division, agreed.

“We are pleased with the court’s decision,” he said in a statement. “The outcome of this litigation recognizes the value of competition in the airline industry.”