Paper Mario vs. Bowser is a goofy Paper Mario manga created at the same time as Pokemon - Quest for Lance (this led to a crossover in Volume 14). It is based off of the first two Paper Mario games and also has original stories (in it's final arc, Bonus).
- Mario, the hero of the manga along with Luigi. Similar to the Super Mario-kun manga, Mario is very mischievous and goofy. Debuts in Volume 1.
- Luigi, the other hero of the manga. Luigi is a lot more serious and often gets hurt due to Mario's "battle strategies". Debuts in Volume 1.
- Yoshi, Mario and Luigi's friend. Yoshi likes to stay at home and visit them when they least expect it. Debuts in Volume 4.
- Goombario, a young goomba who thinks Mario is really cool. He is Mario's friend and follows him around throughout his adventures.
- Goombella, another young goomba friend of Mario. She follows him around after he meets her in Rougeport. Debuts in Volume 8.
- Bowser, the villain of the first chapter and another hero of the second, going along his own path. He acts quite evil but on the inside he is quite a nice fellow. Debuts in volume 1.
- Peach, the princess who was captured by Bowser in the first arc. Despite this, she had her own adventures as a hero around Bowser's castle. In the second game, she is again captured, this time by the Shadow Queen. Debuts in Volume 1.
- Grodus, the villain of the second arc. He is unknown until well into the arc, where he reveals his X-Naut legions. Debuts in Volume 12.
- Shadow Queen, the true villain of the second arc. She has taken Peach and possessed her. Like Grodus, remains rather unknown until her ultimate reveal. Debuts in Volume 13.
- Cranky Kong, an old friend of Marios. He shows up to tell odd stories about the good old days. Debuts in Volume 16.
- E. Gadd, an expert scientist who built a time machine which ended up screwing up time. Debuts in Volume 16.
Main article: List of volumes in Paper Mario vs. Bowser
- Volume 1: A Plea from the Stars
- Volume 2: Bowser's Ruins
- Volume 3: Boo Mansion
- Volume 4: Yoshiland
- Volume 5: Door of Trees
- Volume 6: Shiver
- Volume 7: Bowser's Castle
- Volume 8: Rougeport
- Volume 9: Glitz and Glory
- Volume 10: Battle of the Tree
- Volume 11: Doopliss
- Volume 12: Attack of the X-Nauts
- Volume 13: Palace of Shadow
- Volume 14: Pokemon? Crossover Time!
- Volume 15: Classic Mario
- Volume 16: Tales from Times Past!
- Volume 17: Insane Time Travel!!