At a news conference, Mr. Cooper, a Birmingham lawyer, said gay rights supporters were “working on a strategy now to overcome what has occurred,” and he predicted “significant litigation.” He declined to say how quickly same-sex marriage supporters might return to court.

Legal analysts and lawyers for gay rights groups said challenges could take various forms. Same-sex couples seeking marriage licenses could file suit in federal court, citing Judge Granade’s ruling that the state marriage ban violated the 14th Amendment. Or probate judges who wish to issue the licenses could turn to the United States Supreme Court for an emergency stay, Mr. Krotoszynski said.

The effects of the Alabama court’s ruling were already being felt by couples who had received licenses, like Jason Quarles and Brandon Wright, who were married on Saturday. When Mr. Quarles visited Jefferson County’s courthouse on Wednesday to return the completed paperwork, he said employees told him that his license would ultimately be invalidated. “Our license — or what we were told was a license — was issued legally before any of this came about last night,” said Mr. Quarles, 43.

In Montgomery County, Judge Steven L. Reed, who had been issuing marriage licenses to all couples and was named in the litigation that prompted the State Supreme Court’s order, said that for now, he would only approve paperwork from couples of one man and one woman. “We came to the conclusion that it was certainly binding to me and the other judges that were named,” Judge Reed said of the opinion.

In South Alabama’s Mobile County — where same-sex couples had publicly rejoiced in mid-February over their ability to marry — Probate Judge Don Davis finds himself in a particularly difficult position.

On Feb. 12, Judge Davis was ordered by Judge Granade to issue licenses to four same-sex couples who had sued in the federal court for the right to marry. That day, his office began issuing marriage licenses to any same-sex couple that qualified. As a result, Judge Davis had asked to be dismissed from the case before the Alabama Supreme Court.