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Naruto's naming system always confuses me. Naruto is named Uzumaki, after his mother. But Boruto is named Uzumaki, after his father.

So whose surname is taken while naming a child in Narutoverse? Are there some governing factors?

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  • Naruto's surname was just a special circumstance. Dunno if this was shown in the anime (haven't watched it) but in the manga, this was explained.
    – W. Are
    May 13 at 22:33
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First, lets start off with the facts.

  • Naruto was only named Uzumaki because if he was named Namikaze, that would've put him in great danger.
  • Upon marriage, the wife will usually take the husbands name, for instance, Hinata Uzumaki.
  • On a few rare cases, Sai for example, they will take the wife's name since at no point were they given a last name in the series, like Sai Yamanaka.

As for the naming system, they typically get the fathers name. But as I have mentioned, Naruto being named Namikaze would have put him in great danger as Minato had many enemies who sought his life.

Hiruzen(the third Hokage) Decided to put Naruto's Surname as Uzumaki because the Uzumaki was a clan which has Split after the village was destroyed,which meant that Most of the Uzumakis were refugees, which meant that it would be harder to confirm that Naruto was Minato's child. (emphasis mine)

Well, that's quite all there is to it. It wasn't wanted for anybody to know Naruto was Minato's son. This was to protect Naruto. And as I have previously mentioned, the wife will usually take the fathers name and undoubtedly get the last name of the father, such as Himawari and Boruto Uzumaki.

Although it usually depends on the situation at hand, Naruto/Boruto characters will usually get their fathers name, with a few rare cases, as explained above.


Source

Further reading: Uzumaki Clan

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