Judai Yuki is an ordinary student in Duel Academy, a school where aspiring duelists learn the secrets of Duel Monsters. Although he's a member of Osiris Red, the dorm lowest in the hierarchy, where students fear expulsion due to their low grades, Judai has a grand dream: to become the King of Duelists.
Published in Shueisha's V-Jump in Japan and Shonen Jump in the US, the manga is based on the anime that came before it. Although the main cast and setting remain largely the same, their development in the manga is quite different, as it covers none of the arcs the anime did. The manga also introduces a completely different set of antagonists and villains, following its own continuity.
The first two volumes of the manga cover everyday activities and spars within Duel Academy, exploring the relationships between cards that house spirits and their masters. However, as the series progresses, a darker presence seeking vengeance slowly reveals itself and attempts to infiltrate the school to obtain the spirits.
The manga is written by Naoyuki Kageyama and supervised by Kazuki Takahashi.
- Adaptational Badass: Manjoume often suffers from The Worf Effect in the anime. No such thing happens here. He even manages to defeat Judai in the finals of an official tournament.
- Alpha Bitch: Seika Kohinata fills this role. Unlike most examples of this Trope, she has the skills to back up her ego; in her one duel with Judai, she honestly wasn't bad.
- Beauty Contest: The Miss Academia contest, where a poll to determine the prettiest girl in Duel Academy is held. When Asuka and Seika Kohinata tie for first place, Asuka decides to duel Judai for his vote. She doesn't actually care to win the pageant, however.
- Big Brother Mentor: Judai to Sho. The latter even calls the former "Aniki".
- Light Is Not Good: Reggie MacKenzie, The Dragon (more or less) to Tragoedia. Her deck contains Fairy-Type monsters and celestial beings like Athena and The Splendid Venus, but as far as the villains in the story go, her sadistic nature is second only to Tragoedia himself. Which is fitting, because..
- Dark Is Not Evil: ...the character with the biggest reason to hate her is Midori Hibiki, a sweet, kind, and helpful teacher, who happens to use a deck full of sinister-looking Darklords, the biggest case of this Trope in the story.
- Cheaters Never Prosper: The Starter Villain is Ryuga, a teacher applicant who cheats by using a device that prevents his opponents from using Spell Cards. Judai is put in a tight spot when he's unable to use Fusion, but he manages to turn it around without even finding out what his opponent was doing. Ryuga is never seen after that story; many fans assume he was fired, especially since losing to Judai meant he failed to fulfill the conditions needed to be recognized as an official professor of the school.
- Eleventh-Hour Superpower: During the final turn of the Duel with Tragoedia, Judai summons Ma'at herself to end it by fusing Winged Kuriboh with Light and Darkness Dragon.
- Executive Meddling: Both the anime and the manga had the tail end of the series rushed due to the execs wanting to push out the newer YGO series (Yu-Gi-Oh 5D's and ZEXAL respectively).
- Expy: Tragoedia has almost identical background and motivations with Dark Bakura.
- An Ice Person: Asuka's deck is full of monsters themed around hail, snow and ice.
- Hidden Villain: Most villains related to the main plot are brainwashed pawns of a demon named Tragoedia, who does not actually appear until the final arc.
- Hot Teacher: Ms. Hibiki is a total babe. The trope is rarely brought up, however, usually depicting her as a Cool Big Sis to Jaden.
- Not-So-Innocent Whistle: Judai does this when suggesting that Asuka and Misawa should exchange numbers, saving Misawa the embarrassment of asking her himself.
- Meaningful Name: Seika Kohinata. Her name sounds like the Japanese word for "snake", and she uses a snake-themed deck.
- Mythology Gag: The final chapter of the manga contains many references to the anime continuity. Johan appears in his possessed outfit, Kaiser in his Hell Kaiser garb, Manjoume in his "Black Thunder" coat, and Judai in his Season 4 look. None of these had previously been shown in the manga.
- One Turn Kill: David Rabb pulls this against Asuka.
- "The Reason You Suck" Speech: Judai gives one in the first chapter to Ryuga, who forces his students to surrender their cards if they lose against him.
- Reluctant Fanservice Girl: Asuka practically has to be dragged to the beauty pageant when someone nominates her as a contestant.
- Sadistic Choice: Chronos forces Judai to duel Sho. If he wins, Sho will be expelled, and if he loses, his deck will be confiscated. He decides to win, and it turns out that Sho's 0 on the last test, the reason he was in trouble, was not his final grade.
- Serious Business: While Judai will, like his anime counterpart, duel someone at the drop of a hat, even he is confused as to why Misawa wants to duel him for Asuka's cellphone number, something he's have been glad to simply give him. The reason is, Misawa has a crush on her and thinks they're an item; they aren't.
- Sexy Mentor: Ms. Hibiki in the manga. Her brother Koyo is a male example.
- Throwing the Fight: Reggie neglects to activate her set Mirror Force card (or use her Swords of Revealing Light or even defend with her Seraphim Blaster) during her duel with Misawa during the tournament, which would have prevented his direct attack with Red Ogre which caused her to lose. While it seems out-of-character for a sadist like Reggie to be nice to him, her reason is she simply thinks the tournament is a waste of time, so she bails on it.
- To Be a Master: Judai aspires to duel professionally like his mentor, Koyo Hibiki.
- Yin-Yang Bomb: Manjoume's ace card, "Light and Darkness Dragon". It's even in his name!
- You Monster!: Manjoume calls Tragoedia this after the latter refers to humans as insects. He states he'd rather be an insect than a monster.
- Yokai: Misawa's cards actually have "Yokai' listed as their Type, although the OCG/TCG equivalents are Zombie-Type.