( CNN ) The first day of same-sex marriage turned out to be a mixed bag for Alabama . While many couples converged on courthouses in population centers like Montgomery , Birmingham and Huntsville to exchange vows , other would-be newlyweds -- the majority of them in rural counties -- were turned away . `` It was so joyous to be able to see these couples who had been together for 20 , 30 years to marry and to have their relationship respected , '' said Susan Watson , executive director of the American Civil Liberties Union of Alabama . At the same time , she said , it was `` painful to couples who want to get married and who were denied . '' It 's unclear exactly how many counties issued marriage licenses to same-sex couples after federal courts ruled they could go forward on Monday . Several counties , including Jefferson , Montgomery and Madison ( which have the state 's highest populations of same-sex couples , according to the Williams Institute ) told CNN they were issuing licenses , while others said they were following a Sunday order from state Supreme Court Justice Roy Moore telling probate judges not to issue the licenses because the federal courts lacked jurisdiction . Tuscaloosa County chief probate clerk Lisa Whitehead said the county would follow Moore 's guidance and , `` We will be issuing traditional marriage licenses . '' Likewise , Lee County Judge Bill English said he , too , was `` complying with an order from the chief justice late last night . '' As of late Tuesday , at least 44 counties were not issuing marriage licenses to same-sex couples , while 21 were , said Human Rights Campaign spokesman Ianthe Metzger . His group was still trying to get confirmation on two counties . The ACLU 's Alabama office , which set up a hot line , received complaints from about 50 couples , Watson said . It was widely reported that some counties were n't issuing any licenses . Marshall and Shelby counties ' probate offices told CNN they were in that group . Watson 's organization is now working to obtain a federal court order to explain `` to probate judges that they 're required to follow the U.S. Constitution '' rather than Moore 's order , she said . A hearing is scheduled for 1 p.m. Thursday in the U.S. District Court for Alabama 's Southern District in Mobile , which , incidentally , is one of the counties that reportedly did not issue the licenses . A call to the Mobile County Probate Court was not returned . Mobile County has the state 's fourth-highest population of same-sex couples , according to the Williams Institute , and the ACLU of Alabama is involved in a lawsuit filed by four same-sex couples who were denied marriage licenses in the county , Watson said . Though Watson believes the federal courts were unequivocal in allowing same-sex marriages to go forward in the state , Moore -- who issued his order in response to a U.S. District Court ruling , prior to a similar ruling by the U.S. Supreme Court on Monday -- could n't agree less . In fact , had the Supreme Court ruled on the issue before he sent his order to probate judges , he said he still would have gone through with it . `` The Supreme Court order does n't affect what I said , '' he said . Because the original lawsuit -- filed by a woman who , despite being legally married in California , was prohibited from adopting her partner 's 9-year-old -- targets only Attorney General Luther Strange , the high court 's ruling applied only to Strange , Moore said . And since probate courts fall under Moore 's authority as the administrative head of the judicial branch , he said , judges were free to disregard the U.S. Supreme Court ruling , which declined to extend a stay on Alabama 's prohibition of same-sex marriages beyond Monday . A federal district court and appeals court had also declined Strange 's request to extend the stay . Moore denied Jefferson County Probate Judge Alan King 's assertion that Moore 's Sunday order was akin to then-Gov . George Wallace 's 1963 stand in the schoolhouse door to block integration at the University of Alabama . In Alabama , he noted , Amendment 774 , or the Sanctity of Marriage Act , makes it unconstitutional to perform same-sex marriages or civil unions . It passed with 81 % approval in 2006 . ( A 2012 poll says that approval for same-sex marriage in the state is 32 % , among the lowest in the country . ) `` I 'm not standing in any door . I did not bring this on . This was forced upon our state . This is simply federal tyranny , '' he said . `` This is not about race . This is about entering into the institution of marriage . '' The chief justice , who once lost his post in 2003 for refusing to remove a Ten Commandments monument from a state building in Montgomery , said his decision was not based on his religion . Unlike sexuality , he said , race can not be used to deny someone 's rights . Race is biologically predetermined , where in the case of sexuality , `` people can choose different lifestyles and no doubt they have since Sodom and Gomorrah , '' he said , referring to the cities destroyed in the Bible 's Book of Genesis . The U.S. Supreme Court is expected to address the larger issue -- specifically , whether same-sex marriage in four states deserves the protection of the U.S. Constitution -- later this year . While Moore does n't believe the high court has the jurisdiction to redefine the definitions of family and marriage , he concedes that if the justices rule same-sex marriage is constitutionally protected , Alabama judges would have to honor the unions under the U.S. Constitution 's Supremacy Clause . However , `` I will not concur that that is a proper ruling under the Constitution of the United States , '' he said , explaining his personal beliefs . Watson and other observers believe the Monday decision by the U.S. Supreme Court is a sign of what 's to come when the high court rules on the larger issue . `` I think that tells us something about what we might expect , '' she said . Moore does n't see any writing on the wall . `` I do n't think the ruling is a harbinger , '' he said . `` Justices ( Elena ) Kagan and ( Ruth Bader ) Ginsburg both have performed same-sex marriages . They should both be recused from this case . When you have a predisposition ... you have no right to sit on the case . They 're flouting the ethical rules that apply to most judges in this country . '' CNN 's Devon M. Sayers contributed to this report .
It 's unclear how many counties declined to give licenses to same - sex couples . Chief Judge John Moore is telling probate judges to not ` ` federal law '' ACLU seeks order for probate judges to honor same - sex marriages .