Deputy Clerk Brian Mason issued the license to Shannon and Carmen Wampler-Collins, a couple who met 23 years ago at Smith College. Davis never left her office during the process.
Instead of her name appearing on the license, it said it was issued pursuant to a court order and under the authority of the city of Morehead, Kentucky.
A preacher at the back of the room tried to shout the couple down, urging them to repent and not get the license.
The couple's supporters tried to drown him out, chanting, "Love Has Won."
As Davis returned to work this morning, she spoke at a news conference, asserting that the licenses were being issued without her authority and she wanted her name and title removed.
Davis said she was faced with a "seemingly impossible choice ... my conscience or my freedom."