At the start of a three-week trial in Boston, Justice Department attorney William Jones said the Northeast Alliance, unveiled in July 2020, is a "de facto merger" of American and JetBlue's operations in Boston and New York.
Hayes acknowledged that he had been critical of previous joint ventures similar to the Northeast Alliance.
The trial started after a week in which U.S. judges ruled against the government in two antitrust fights: sugar and insurance.
JetBlue is pursuing a $3.8 billion acquisition of low-cost rival Spirit Airlines (SAVE.N), subject to antitrust review.
Hayes has said that no matter how the fight over the Northeast Alliance ends, it would be good for JetBlue's effort to buy Spirit.