The post coincided with a surge in the hashtag #JeanMichelTrogneux on Twitter and other networks.
Mrs Macron finally broke her silence on the conspiracy theory last month, telling RTL radio: "At first I watched this from afar. I had heard of it but, well…"
"And then at one point, I realised that they had changed my family tree," she went on.
"For three quarters of my family, everything was fine, then all of a sudden, you get to my brother and I'm my brother. They played with my parents' genealogy and that's not possible," she said, adding that she would press for charges.
She said there were "three levels" of people involved, the first were "women who sent the messages and who have apparently been pursuing me for some time".
"Then there are those who relay and amplify, then there are the hosts".
The false claim reportedly first appeared in far-Right magazine Faits et Documents (Facts & Documents) but went relatively unnoticed.
But when "correspondent" Natasha Rey - who contributes to the journal and has a history of attacking the Macrons on Facebook - gave an interview on YouTube in December, the allegations went viral online.
In the interview, she referred to an old Trogneux family photograph. While the little girl sitting on her mother's knee was Mrs Macron, the journalist claimed she was in fact his brother, the boy in the checked shirt in the photograph before "he" became a transgender woman and underwent a sex change operation in the early 1980s.
Websites linked to the far-Right, anti-vaxxers, the Yellow Vests anti-government movement and QAnon extremists, who believe the US is in the grip of devil-worshipping child abusers, spread the false claims.
Confirming she had filed for charges, Mrs Macron, a vocal supporter of efforts to tackle harassment in school and on social media, said: "If I do nothing when I've been against harassment for the past four years, I'm not audible. People will say you have done nothing." She said that even as First Lady, removing the rumours proved an uphill struggle.
"It took me five and a half days to get rid of this rumour with a lawyer who is specialised in this area," she said, adding that many people facing damaging allegations online were left powerless.
The legal action comes ahead of the French presidential election in April. Mr Macron has not yet declared his intention to seek re-election but he is widely expected to do so.
Emmanuel Macron's relationship with his wife 24 years his senior, whom he met while she was a teacher and he was still a teenager, has been a source of media attention in France and abroad.
It is not the first time the couple have been targeted by rumours about gender or sexual orientation. During the 2017 presidential campaign, Mr Macron denied claims that he was gay.
The attack on Mrs Macron has led to fears of the "Trumpisation" of political debate in France, with fake news circulated to potentially sway voters, particularly by the far-Right who already enjoy widespread popular support.
In anticipation, the French government recently launched Viginum, a 30-man agency tasked with protecting the presidential campaign from "foreign digital interference".
In 2017, the Macron camp blamed Russia for a hack attack in which confidential campaign emails were released online.
The leak failed to dent his electoral chances. According to its director, Gabriel Ferriol, the agency's main aims are to root out any "smear campaign or the promotion of a candidate coming from abroad" as well as attempts to dissuade voters from turning out.
