Since 1994, Gabino Zavala reigned over the San Gabriel Region in the nation's most populous archdiocese.
That came to an end Wednesday when the Pope Benedict XVI accepted the 60-year-old bishop's resignation.
In a letter to the faithful, Los Angeles Archbishop Jose Gomez said Zavala told him in December that he had two children who live with their mother in a different state. Both are boys in their early teens.
"The Archdiocese has reached out to the mother and children to provide spiritual care as well as funding to assist the children with college costs," Gomez said. "The family's identity is not known to the public, and I wish to respect their right to privacy."
Zavala did not return calls seeking comment.
The doors to Zavala's pastoral center office were locked Wednesday and employees there weren't talking about the scandal. Archdiocesan spokesman Tod Tamberg says it appears Zavala had a consensual affair with an adult but he has no other details.
"It came to me as a surprise when early in the morning I went to open the email and I found the communication from the Archdiocese," said Joseph Canna, pastor of Our Lady of Guadalupe, which is on the campus shared with Zavala's office. "I am saddened by the event and I pray that he is all right and we will overcome this problem."
Coming after years of scandals in the Catholic Church involving priest abuse, the Bishop's admission stunned area Catholics.
"I was in shock," said Ashley Lopez. "I didn't say anything. I was just with my mouth open, like 'Are you kidding me?'"
In his position, Zavala was in charge of 66 parishes in an area that stretches from East Los Angeles to Pomona to the San Gabriel Valley.
The Vatican will choose a replacement.