Top New York chef Gabrielle Hamilton, who owns popular East Village restaurant Prune, has been having a secret affair with her sister’s husband, we can exclusively reveal.

The 2011 James Beard Award Best Chef in New York City winner wrote a recent best-seller about her stint as a lesbian before marrying Italian doctor Michele Fuortes, a teacher and researcher at Weill Cornell Medical College. The book describes a troubled marriage. But Gabrielle, 45, does not mention she has been cooking up an affair with her sister Melissa’s architect husband, Michael Hagerty.

Gabrielle split with Fuortes last month after she admitted she was still having a fling with her brother-in-law. A source told us, “The family is torn apart, with Gabrielle’s husband and sister refusing to speak to her or Michael.”

A source said the spouses believe the romance started in the summer of 2010, when Gabrielle spent a few weeks on vacation at Melissa and Michael’s house in New Jersey. After a few months he told his family he was moving out.

“After Gabrielle’s book tour in May, her sister found out and confronted her husband,” the source said. “Gabrielle told her husband about the affair. But she said it was the biggest mistake of her life and convinced him to go on a family vacation to Italy. But in September, she confessed she had restarted the affair.”

Gabrielle, who has two sons with Fuortes, told us the story of the affair was “not true” when we first called about it in May. She didn’t respond to us this month.

Refusing to comment on the affair, Fuortes told us: “Since Gabrielle’s great success with her restaurant and her wonderful book, I made a policy of not talking to the press about my wife, her cooking or her book (all things that I deeply love).” Gabrielle’s sister Melissa, a cookbook publisher and former Saveur editor who has two daughters with Michael, said, “I will not comment on issues relating to my family’s private life.” Michael didn’t respond.