I've already looked through the forums, but I can't find a manga that fits what I'm looking for.

I want to read a manga where the protagonist has to keep his/her identity a secret from everyone in his/her life, including his/her parents. I would also like for the antagonist to be unaware about the protagonist's identity at the beginning, but later finds out about it.

Genre: Preferably shounen, but it's okay if it's not. No yaoi, yuri, or smut.

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Sounds like a superhero....
Anyway, my favorite is Basara, though it's not shounen.
After going through the search engine: This is what I get

eyeshield 21 fits that bill pretty well though it is too long for my tastes and it's seinen, you've probably already read it but it's good

Akumetsu

Yu Yu Hakusho. Though his identity isn't secret, his occupation is.

Death Note.

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I second Basara. It suits your request perfectly, except for the parents thing. (protagonist doesn't have parents) Although, she keeps it hidden from her parent figures, which should fulfill your request. Even though it is shoujo, it's not stereotypical-romance-cheesiness that most shoujos are. The romance actually doesn't rule the story. 😃

Good luck!

Luca, the Summer I Shared with You

Bokurano

Try Superior

I third Basara

1/2 Prince

I second Superior
R-18 is okay, I guess, not exactly my style, but it does qualify.

1/2 prince is exactly like that cuz its about a girl who goes into a virtual reality game as a guy and many of her friends don't find out till the middle

Prince: Infinite Xity!
Infinite City: Aj Plau!
what does it mean?

Assassins Creed III
Do you Seriously think i CARE?

Well, they may not be a perfect match, but how about ...

• Oresama Teacher (Shoujo, but not stereotyped)

The main character is a former delinquent and has to transfer schools. Her mother orders her to behave and to start a new life, but again and again she is back to her usual self, even if she tries her best to cover things up for most of the people around her.

• Dendrobates (Seinen)

Sengawa works actually as an accountant for the police, while he is an assassin and gets his equipment out of the archive.

• Bloody Monday

• Tiji-kun!

"It's like love is a bonus in your life. Even without it, I'm just fine. I don't feel like pointlessly searching for it. You don't have to make yourself unhappy." (Ookami Shoujo to Kuro Ouji)

"Why does it rain?" - "To create drama." (Drops (Andou Yuki))

I third Superior... I really love it~!
also I second Oresama Teacher and 1/2 Prince... really awesome :3

My list (all of them are girls as the main lead... except Yankee-kun to Megane-chan);
Fly High! - the girl hides (at the beginning) that she's strong and trained in the mountains for 6years~!(but her parents know 'bout it..)
Red Lion - it's awesome. the girl, after being expelled, hides that she was a well-known delinquent (her parent know about it too)
Alyosha! - the girl was a hidden assassin... now she wants to live a normal live (she doesn't have parents)
Yankee-kun to Megane-chan - she might look like a normal nerdy girl.... but she was a delinquent! (not sure if she still have parents... but I think yes and they do know about it)
Gokusen - she is a nerdy teacher (I personally duislike the style of the drawings.. but the story is awesome!).. but hey hey, She's a head of Yakuza Family!?
Beauty Pop - the girl hides her talent of being an awesome hairstylist....
Arisa - the girl is disgusted as her twin 'cuz her twin tried to commit suicide! Wait... WHAT?!
9 Banme no Musashi - where the girl is working under covers because of her missions~
Kaichou wa Maid-sama - all tough and rules over the boys but.... She works in a cafe?! and one of her classmates found out?!?!

well... I have a lot more but i'm too lazy to find the titles... so if u want them just tell me ^o-
I hope I was of any help <3

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Black haze ( The guy became famous dark magician when he activated his power but only 2 people know about it that his true identity looks like a little kid.)
ULTIMATE LEGEND: KANG HAE HYO- The ML lose his memory after an accident and got bullied after he transfer to a new school but the truth is that he the most fearsome "Grim reaper" in his province...

D