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In Captain America: Civil War we see Peter Parker come home to see Tony Stark chatting with his Aunt. Later he tells Peter that he knows he's Spider-Man, and that he wants to recruit him.

How does Tony Stark know that Peter Parker is Spider-Man?

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    A huge incentive for Tony to have top-shelf surveillence and identification is he's not the only player in the game. HYDRA, various governments, etc. are also out to recruit powered people. What amazes me is how the new Ant-man was a surprise to Stark/Avengers, they didn't watch Pym's house? – Harper Nov 9 '17 at 23:15
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    @Harper - Perhaps Hawkeye was the one watching Pym's house. – T.E.D. Nov 10 '17 at 10:59
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    I find it more surprising that everyone hasn't discovered the secret identity of these characters. A secret identity is a fragile thing when you are constantly putting yourself in the spotlight the way these characters do every day. Eventually someone would see something. – R. McMillan Nov 10 '17 at 13:35
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    How Batman keeps his identity a secret? I don't know! I just don't know! – ibrahim mahrir Nov 10 '17 at 15:26
  • @R.McMillan Who do you mean by "these characters"? Steve Rogers is a decorated war hero and everybody knows he is Cap, Thor is just Thor, Black Widow and Hawkeye don't have secret identities, those names are basically just callsigns. And Tony blurts out he's Iron Man in that press conference... Witch and Vision don't hide their identity either and Banner being Hulk is not really a disguise anymore since the CGI-face now actually looks more like Ruffalo. So which Avenger actually has a secret identity in the MCU? – BMWurm Nov 13 '17 at 13:59
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In short: He is a multi-billionaire genius and has sources, but here is what the official person who worked on the film said:

And from geektyrant:

So how exactly did Stark know about Peter Parker, a.k.a. Spider-Man? During an interview with ComicBook.com Markus offered a pretty cool explanation.

"I think he's been keeping tabs. I think he might know about everybody." I imagine when he says “everybody” it also means the characters in the Netflix series like Daredevil, Jessica Jones, Luke Cage, Iron Fist and The Punisher. I mean, how can he not know about those guys, right?

He continued:

"Tony has A.I. somewhere running crime statistics. He can see where it's going up and heroes might be needed and where it's going down and there might be heroes. It's why he built Ultron in the first place."

Similar statement given on cinemablend too.

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    so, basically, he is marvel's batman now. Dead parents? Check. Lots of money? Check. Gadgeteer type of hero? Check. Has supercomputer that let's him know everything about fellow heroes? Check. Has a butler? Well, had (later upgraded to love interest, apparently), but check. – Mr Scapegrace Nov 9 '17 at 14:59
  • But how does having huge amount of info about crime, help him "see under the mask"? – Plexus Nov 9 '17 at 15:32
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    @MrScapegrace actually, in comics, Stark had a butler named Edwin Jarvis , very similar to Bruce Wayne's Alfred Pennyworth, – Vishwa Nov 9 '17 at 16:34
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    Does Tony Stark know Batman is Bruce Wayne??? – ibrahim mahrir Nov 10 '17 at 15:29
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    Quis custodiet ipsos custodes... – DevSolar Nov 10 '17 at 17:05
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Although Ankit Sharma's answer is correct, the user Plexus asked a good question: "But how does having huge amount of info about crime, help him 'see under the mask'?" I started replying to his comment, but my reply got too long, so here goes.

The way I see it, having a huge amount of money plus advanced technology lets Tony Stark spy on people. Peter Parker had to get in and out of the Spider-Man costume, so Tony Stark would just check all his surveillance footage of Spider-Man until he could watch the costume change.

After that, he could use facial recognition to find out where this unnamed kid lives, where he goes to school, etc. Knowing that information would make it simple to narrow down which name is his (only kids who go to that school, only people who live in that apartment building, etc.). Tony also could have used lip-reading software on the friends / teachers / family around Peter: when they said Peter's name, Tony could capture it.

In a nutshell: through surveillance and possibly-fictional analytic software, Tony could figure out Peter's name and where he lives.

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    There has been a lot of fuss in some papers about how Facebook links different people (or different aliases of the same person) when there is no link that Facebook should be able to access. I am not sure that the analytical software needs to be fictional. gizmodo.com/how-facebook-outs-sex-workers-1818861596 – Tony Dallimore Nov 9 '17 at 21:35
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    "until he could watch the costume change" - or until he saw the house that Spiderman liked to return to (then no facial recognition needed, just public records), since Peter frequently changes costume in his bedroom instead of out on the streets. – Remy Lebeau Nov 9 '17 at 23:20
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    You're alleging that Tony Stark has mass surveillance so he can watch highschoolers changing clothes?? "I wonder who Spiderman is - Jarvis, follow him home with a drone, and look up the address in the yellow pages". Quicker, easier, cheaper, less creepy. – TessellatingHeckler Nov 9 '17 at 23:43
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    hmmmm. According to the Marvel Animated wikia (which I admit to having no clue to its veracity), Pete's spidey-sense should've prevented his being seen while costume changing - and possibly other times - if being seen would be dangerous. Although the article then goes on about a bunch of ways that it wouldn't kick in I'd expect a drone surveilling him to invoke it. – mcalex Nov 10 '17 at 8:35
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    @mcalex Perhaps. But he's also portrayed as a reckless teenager. He might worry about changing in front of someone but not a camera; or he also may simply feel safe at home, and ignore his "spidey sense" – jpaugh Nov 10 '17 at 20:33
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I believe the Answer is quite simple. It was S.H.I.E.L.D.'s (Hydra's) 'Project Insight'. S.H.I.E.L.D.'s goal was to identify and locate/neutralize terrorist threats, HYDRA's goal was to identify & locate/neutralize anyone who might work against them especially super powered individuals. It would have known about anyone with an altered DNA. I imagine whatever method they used was probably Stark technology, but regardless he had access before S.H.I.E.L.D. was disbanded, or he found out by analyzing the data agent Romanov leaked, or he hacked/accessed the technology after S.H.I.E.L.D. was disbanded, maybe when he hacked the tech when he was on board the heli carrier, no telling what Jarvis got for him when he did that. Stark could have put back doors into a lot of S.H.I.E.L.D. technology he is that kind of person.

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This is what I saw in Spider-Man: Homecoming, in this movie, Tony Stark saw lots of videos of Spider-Man on internet. He used to operate in only one area. So according to Tony Stark's data for that area, only Peter Parker matched the description. So he stalked him for a while and hence confirmed that Peter Parker is a Spider Man.

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