The state of Alabama has started granting marriage licenses to same sex couples following a Federal District Court decision deeming the ban against same sex marriage unconstitutional but some legal issues are muddling the law's implementation.

Among those who received the first licenses in Jefferson County were Dee and Laura Bush, who have been together for seven years.

"It is great that we were able to be part of history," Dee said as she and her partner proceeded to a waiting minister in a park, ready to perform the marriage ceremony.

While some members of the LGBT community celebrate their victory, Alabama's Chief Justice Roy Moore has issued his own order to prohibit judges from pushing through with the granting of the licenses, something that has caused a huge amount of confusion among probate judges in Alabama.

In Moore's statement, he said the ruling "raised serious, legitimate concerns about the propriety of federal court jurisdiction over the Alabama Sanctity of Marriage Amendment."

Earlier reports indicated that the Federal Court's ruling was postponed until Monday to prepare the state for its implementation. Petitions by the state attorney general to extend the postponement to further appeal the ruling was denied.

As of Tuesday, 44 of Alabama's 67 state counties were refusing to grant the marriage licenses, prompting the Federal Court to set a hearing to determine what measure to take on those who are still resisting its decision on same sex marriage.

Judge Greg Norris, the Probate Judge in Monroe County, who heads the Alabama Probate Judges Association, initially refused to grant the licenses but changed position and emailed his colleagues to explain his decision, despite not being in favour of the court ruling.

"The law says I may perform  them (gay mariages), and I just don't want to do it," he said. "I'm going to follow the law to the best of my ability."

However, there are still some judges who remain firm against the order until a higher authority makes the guidelines clear.

In a press statement, Mobile Alabama Probate Judge Don Davis said that he is committed to upholding the law, barring conflicts between the federal and state courts.

"[B]ut we are dealing with unprecedented conflicts of law between the federal and state courts and I must be certain that any action I take is fully compliant with the law, both the United States Constitution, as well as the Constitution and statutes of the State of Alabama."

The Federal Court ruling to allow marriages between same sex couples makes Alabama the 37^th state to recognise gay marriages.