New York City Ballet, which has been going through one of the most tumultuous periods in its history, announced Thursday that it had picked new artistic leaders for the first time in more than three decades, turning to a pair of respected former dancers to help right the ship.

Jonathan Stafford, 38, who has been running the company for more than a year on an interim basis, will become the new artistic director of City Ballet as well as its affiliated academy, the School of American Ballet. Wendy Whelan, 51, a star ballerina who danced with the company for 30 years, will become City Ballet’s associate artistic director. The two said they intended to work as partners.

They are taking over a company that has been shaken over the past year and a half. Peter Martins, its longtime ballet master in chief, abruptly retired early last year amid allegations of physical and emotional abuse, which he denied. Then, with the company being led by an interim team overseen by Mr. Stafford, three of its 14 male principal dancers were forced out after being accused of sharing text messages of sexually explicit photos of women.

[Read more about the turmoil at City Ballet. | Read about the search for new leadership.]

Mr. Stafford and Ms. Whelan, whose appointments were announced at a meeting of the company on Thursday morning, said that healing the rifts within the company and improving its backstage culture would be a big part of their work.