Since the anime and manga differ for Yu-Gi-Oh!, I figured I'd make this list.
I know there are more manga, but I don't think they are on MAL. Please consult places like Yugipedia for more complete lists.
Manga, 38 vol, 1996
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The original manga by Kazuki Takahashi. This is basically the only Yu-Gi-Oh! where the manga is the basis for the anime. The other ones tell a different story not related to the anime.
The Toei anime (Season 0) adapts up to chapter 59 (Monster World).
The first Gallop anime (Duel Monsters) adapts from chapter 60 (Duelist Kingdom).
In both anime there were significant alterations to the plot. Because of this, the Dark Side of Dimensions (DSOD) movie is a sequel to the manga.
Manga, 5 vol, 2004
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Akira Ito, who later became co-creator of Cardfight Vanguard, wrote and drew this spin-off under the supervision of Kazuki Takahashi.
READ AFTER FINISHING MANGA DUELIST KINGDOM
Manga, ? vol, 2016
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The only other story written by Kazuki Takahashi on this list (besides the original).
POST OG MANGA SET UP FOR DSOD
Manga, 9 vol, 2005
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Written and illustrated by Naoyuki Kageyama, who later did art for Cardfight!! Vanguard: Turnabout and writing + art for Cardfight!! Vanguard: will+Dress D2.
One-shot, ? vol, 2014
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Also by Naoyuki Kageyama.
Read after the main GX manga.
Manga, 9 vol, 2009
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First time Masahiro Hikokubo, who is credited for Duel Composition in most of Yu-Gi-Oh!, wrote a Yu-Gi-Oh! manga.
Art by Masashi Satou, who also went on to write some of the other Yu-Gi-Oh! manga.
Manga, 9 vol, 2010
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The series composer of Season 4 of GX, Zexal and VRAINS; Shin Yoshida, was in charge of writing this one. Yes, the series composer of Zexal, wrote another version of Zexal.
Art by Naoto Miyoshi, who went on to make more art for Yu-Gi-Oh!, including the character designs for Arc-V.
Kazuki Takahashi designed the characters for Zexal, but he left after conceiving the concept. He came back for DSOD.
Manga, ? vol, 2012
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Written and drawn by Akihiro Tomonaga, who later went on to make Saikyou Duelist Yuuya!!
Manga, 7 vol, 2015
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Just like the Zexal manga, Shin Yoshida is the writer and Naoto Miyoshi is the illustrator. Only this time Naoto Miyoshi also did the character designs and Masahiro Hikokubo is credited for duel composition.
One-shot, ? vol, 2014
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Special one-shot written and illustrated by Naoto Miyoshi, who also did character design and art for the main Arc-V manga and anime.
Manga, 2 vol, 2015
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Written and drawn by Akihiro Tomonaga, who also made D Team Zexal.
Manga, ? vol, 2019
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Story and art by Masashi Satou, who previously illustrated the 5Ds manga.
One-shot, ? vol, 2020
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One-shot by Masashi Satou, who previously illustrated the 5Ds manga and wrote and drew the OCG Structures manga.
Manga, 3 vol, 2020
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Story written by Masahiro Hikokubo, who previously wrote the 5Ds manga.
Illustrated by Tsubasa Sugie.
Manga, 4 vol, 2022
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Written and illustrated by Naoya Sugita.
Manga, ? vol, 2022
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Once again, Shin Yoshida is the writer and Naoto Miyoshi is the illustrator.
