The American conductor Gavriel Heine has been a fixture at the Mariinsky Theater in St. Petersburg, Russia, for 15 years. He has led hundreds of performances of classics like “Swan Lake” and “The Rite of Spring.” And he has done so as a protégé of the company’s leader: Valery Gergiev.

On Saturday, Mr. Heine went yet again to the Mariinsky, but not for an evening at the podium. He was there to inform Mr. Gergiev — a longtime friend and supporter of President Vladimir V. Putin of Russia — that he was resigning from his post as one of the state-run theater’s resident conductors. Mr. Heine gathered his possessions, including a few white bow ties and scores for “La Bohème” and “The Turn of the Screw,” and prepared to leave the country.

Mr. Heine, 47, had been increasingly disturbed by the Russian invasion of Ukraine. “There’s no way I could ever be in denial of what is happening in Ukraine,” he said during a series of interviews over the past week. “Russia is not a place where I want to raise my son. It’s not a place where I want my wife to be anymore. It’s not a place I want to be anymore.”

His resignation comes as the war continues to upend performing arts. Cultural institutions in Europe and North America, vowing not to hire performers who support Mr. Putin, have severed ties with some artists — most notably Mr. Gergiev — as well as orchestras, theaters and ballet companies. Many artists, citing the invasion, have canceled appearances in Russia.

Mr. Gergiev, the theater’s general and artistic director, was once one of the world’s busiest conductors, but his international career has crumbled. Carnegie Hall, for example, canceled a pair of concerts of the Mariinsky Orchestra under his baton that had been planned for May, after he had been dropped from a series of Vienna Philharmonic performances in February. He has returned in recent weeks to St. Petersburg to focus on that company and his domestic cultural empire, which encompasses several stages, thousands of employees and tens of millions of dollars in state financing.

Mr. Heine found Mr. Gergiev at the Mariinsky on Saturday, where he was leading rehearsals and performances of Wagner’s “Götterdämmerung” and Verdi’s “Attila.” He described repeatedly trying to catch his mentor backstage to inform him of his resignation, finally cornering him in an elevator.

It was a quick conversation: five minutes while Mr. Gergiev was rushing to a meeting. Mr. Heine said that Mr. Gergiev seemed surprised but accepted his decision.

“He was very nice to me,” Mr. Heine said. “He gave me a handshake and a hug and wished me well. And of course I thanked him for giving me such a huge chance pretty early in my career.”

The two conductors also spoke about recent tensions between Russia and the West. Mr. Gergiev — who was fired from engagements in the United States and Europe, as well as from the podium of the Munich Philharmonic, over his refusal to publicly condemn the war — defended his decision, saying that he was not a child, Mr. Heine recalled.

The Mariinsky declined to comment on Monday, and said it could not yet confirm Mr. Heine’s resignation. However, the company removed Mr. Heine’s biography from its website Monday evening.

Mr. Heine’s departure from the Mariinsky is an unexpected conclusion to his three-decade career in Russia, where he studied with renowned teachers and rose to become a conductor at one of the country’s most prestigious houses. And his exit is another blow to Russian cultural institutions, which are grappling with boycotts and cancellations by foreign groups as the country’s arts increasingly turn inward under Mr. Putin. Mr. Gergiev remains a critical figure in Mr. Putin’s campaign. Mr. Putin, during a televised meeting last month, asked Mr. Gergiev whether he was interested in the idea of uniting the Bolshoi Theater in Moscow with the Mariinsky, an arrangement that would take Russia back to the days of the czars.

“Russia is just going to be more and more closed,” said Simon Morrison, a music professor at Princeton University. “It’s going to revert more and more to its own true self, harsh as that might seem — a sealed-off, angry, paranoid and resentful feudal realm.”

Mr. Heine, who grew up in Cherry Hill, N.J., became interested in Russian culture as a teenager. He accompanied his mother, a pianist, to a performance in Moscow, and while there took cello lessons with a professor at the Moscow Conservatory.

After high school, he returned to Russia for language and cultural studies. In 1998, he became one of the Moscow Conservatory’s first American graduates, then began to study with the eminent Russian conductor Ilya Musin, who also taught Mr. Gergiev.

His break came in 2007, when Mr. Heine approached Mr. Gergiev during a rehearsal in Philadelphia and asked him whether the Mariinsky had any openings. Mr. Heine was invited to make his debut at the theater later that year with Mozart’s “Le Nozze di Figaro,” and soon began to lead performances there regularly. In 2009, he was named a resident conductor.

During his time at the Mariinsky, Mr. Heine was at the podium for over 850 performances and watched as the company grew in power and size under Mr. Gergiev. The arts and the state, Mr. Heine said he came to understand, were inexorably linked in Russia. He was in the theater on two occasions when Mr. Putin, the house’s main benefactor, appeared for awards ceremonies and other events.

“I just assumed that culture is a priority for this government, for whatever reason,” he said. “And they feel very strongly about it, and that’s the relationship.”

He recognized that Mr. Gergiev sometimes used art for political purposes, such as when he led a patriotic concert in the Syrian city of Palmyra in 2016, shortly after Russian airstrikes helped drive the Islamic State out of the city.

Still, Mr. Heine said, he was not bothered by Mr. Gergiev’s long association with Mr. Putin. The two have known each other since the early 1990s, when Mr. Putin was an official in St. Petersburg and Mr. Gergiev was beginning his tenure at the Mariinsky, which was then called the Kirov Theater.

“I never felt that we were at the service of the state,” Mr. Heine said. “It just seemed like the state trusted Gergiev for his artistic priorities, and he convinced them that his priorities were good priorities, and they funded that.”

The invasion of Ukraine changed his views on Russia and his place in it. He had a personal connection to Ukraine, having served as chief conductor of the Kharkiv Symphony Orchestra there from 2003 to 2007. When he saw images of Russian missiles hitting a building in Kharkiv in early March, he was distraught.

“That broke me,” he said. “I saw the faces of all of the musicians that I had worked with. I thought of my orchestra director who lives two blocks behind that building. I mean, that’s his neighborhood. I just lost it. I couldn’t do anything that day and I thought that was pretty much it.”

He resolved to leave his position, in part because he was worried about the safety of his wife and 11-year-old son. His family left for the United States in early March, while he went to Switzerland to lead a production of Tchaikovsky’s “Eugene Onegin” at the Opéra de Lausanne.

He returned to St. Petersburg last week and spent several days packing up his apartment and saying goodbye to colleagues over meals at his favorite Italian restaurant near the Mariinsky, where a pizza is named for him. He submitted his resignation letter to the company on Sunday and returned the keys to his locker.

On Monday, he arrived in London, where he is set to lead a production of “Swan Lake” at the Royal Opera House next month.

He said it was hard for him to leave Russia, where he has spent about half of his life. He considers himself Russian from a cultural perspective, though he remains an American citizen.

Still, Mr. Heine has made his peace with moving on. “The sad part wasn’t walking into the theater; the sad part was the disappointment and the sadness of the people that I had to tell I was leaving,” he said.

“The theater’s not going anywhere,” he added. “I am.”