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After the death of his older brothers, Aemon was the true heir to the throne. Unfortunately, he refused the throne. Who knows, maybe Targaryens would still be ruling if he didn't join the Watch.

My question is: Is there anybody who still remembered him during Robert's rebellion and after it? Did Robert know? He wanted all Targaryens dead.

And also: Back in season episode 1, Robert and Ned speak in the crypts of Winterfell.

Ned: It's over, your grace. Targaryens are gone

Robert: Not all of them.

Immediately after that we see a scene with Daenerys and we can assume he was talking about her. But is it possible he meant Aemon?

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    He wasn't the heir, having sworn not one but two oaths to neither inherit nor sire.
    – Paul
    Aug 10, 2017 at 12:12

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Aemon and Rhaegar were corresponding before the Rebellion, so he was not forgotten. It was just that Aemon was not a direct threat. Maester Aemon, being a Maester and member of the Night's Watch, could not inherit title or lands, and couldn't have children. Plus, he was already quite old during the Rebellion.

Finally, killing the Maester of the Night's Watch breaks the neutrality between Night's Watch and the Crown, making the move not very popular.

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    As a follow up the fact that Robert sent assasins to kill Daenerys and then changed his mind after persuasion by Ned shows that those where the Targaryen's he meant. In addition as stated Aemon was now a Nights Watchman, any attempt to leave the Watch even to try to claim the throne would have seen him killed as a Deserter of the Watch by anyone he tried to rally to his banner.
    – Richard C
    Aug 10, 2017 at 12:19
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    Plus, Robert consider to kill dany only once she is with khal drogo, not before. He did not want all targaryen dead, only the one who claim the throne
    – Kepotx
    Aug 10, 2017 at 12:27
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    But Robert also said in his conversation with Ned in episode 2 "I'll kill every Targaryen I get my hands on". That doesn't sound like "I'm fine with those who don't claim the throne". Was Robert aware of Aemon's existence?
    – Martin
    Aug 10, 2017 at 12:48
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    @Martin Robert wasn't a dishonorable man. He was soul of chivalry for earliest parts of his reign and thats when he decided he won't bother Aemon. Aemon was part of the Night's Watch. So he was protected by neutrality of NW. Everyone knew about Aemon. Stannis also called him out when he came to Castle Black.
    – Aegon
    Aug 10, 2017 at 13:02
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    @PlutoThePlanet It was Viserys being paranoid, Robert never sent any assassins until she got pregnant. Robert admitted it that he should have had them killed but made the mistake of listening to Jon Arryn and then they were sheltered by Illyrio and protected by unsullied guardsmen in his manse, making the deed impossible. So it is clear, it was Viserys' paranoia and Dany believing it.
    – Aegon
    Aug 10, 2017 at 15:38
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TL;DR - I doubt many common-folk or even high-lords Maester Aemon's lineage due to the vows he swore and his advanced age was not much a thought by those playing the game of thrones.

First a brief history...

Aemon was the third son of King Maeker I and as such decided to train as a Maester as he would not likely inherit the throne. The decision also was cemented because a Maester is stripped of their family name, titles, etc. once they forge a chain. This did not stop some from trying to elevate Aemon to king during the Great Council of 233 AC. During this time Aemon decided to join the Night's Watch to swear a second vow of holding no titles to further remove himself from the politics of Westeros.

So it is likely that the following groups or people knew of Maester Aemon:

  • The Night's Watch: Jeor Mormont, and therefore likely others higher in the Night's Watch ranks. Jon also figures out Aemon's true lineage after some conversations.

    Aemon knew, and rightly, that if he remained at court those who disliked his brother's rule would seek to use him, so he came to the Wall. And here he has remained, while his brother and his brother's son and his son each reigned and died in turn, until Jaime Lannister put an end to the line of the Dragonkings.[Jeor Mormont to Jon Snow] - A Clash of Kings - Jon I

  • The Maesters of the Citadel: We see Alleras and Marwyn know of Aemon's history.

    He was more than just the oldest living maester. He was the oldest man in Westeros, and lived through more history than Archmaester Perestan has ever learned. He could have told us much and more about his father's reign, and his uncle's. [Alleras to Samwell Tarly] - A Feast for Crows, Samwell V

    The world the Citadel is building has no place in it for sorcery or prophecy or glass candles, much less for dragons. Ask yourself why Aemon Targaryen was allowed to waste his life upon the Wall, when by rights he should have been raised to archmaester. His blood was why. He could not be trusted. No more than I can. [Marwyn to Samwell Tarly] - A Feast for Crows, Samwell V

Since these are the organization Aemon is directly associated with this makes sense. I have not found any evidence that other people in the realm, even King Robert knew of Aemon's lineage.

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  • IIRC, Aemon mentions to Jon that he has not confided his Targaryenism to most people.
    – Möoz
    Aug 10, 2017 at 23:51
  • @Möoz He didn't say that. He just told Jon that he uses only his first name as per vows of his order which compel him to give up his last name. High officers and those who knew him must have known. Jeor Mormont knew without a doubt.
    – Aegon
    Aug 11, 2017 at 6:38

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