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Ginko /YokiThe main protagonist. A wandering Mushishi, or Mushi Master, Ginko travels the land solving the troubles of those afflicted with mushi-related illnesses. His analytical mind and somewhat unique stance of 'live and let live' when it comes to mushi makes him rather effective at his job.
- All-Loving Hero: Ginko is a firm believer that all things have a right to live, and does his best to preserve the lives and happiness of both the people and mushi he comes across.
- Amnesiac Hero: Ginko has no memories of his early childhood, because of a powerful mushi that wiped his memories and devoured one of his eyes, turning his hair white and his remaining eye green in the process.
- Badass Pacifist: Ginko refuses to harm the mushi unless he absolutely has to, but this doesn't stop him from being extremely successful at his job.
- Crazy-Prepared: Travels around with a large, wooden backpack containing all the equipment he needs to deal with the mushi.
- Dark and Troubled Past: Ginko has been wandering for as long as he can remember, as he attracts mushi with his mere presence and thus can't stay in any one place for long. It's even mentioned that a few unscrupulous mushishi took him in to use as mushi bait so they could attract more customers.
- Ignored Expert: It's practically a running joke of the series. Ginko is one of the most intelligent and efficient Mushishi in all of Japan, if not the world, and he is well known for his work. That being said, the conflicts of most episodes stem from one of the following:
- Ginko warns a person that something bad will happen if they do 'x'. The person proceeds to do 'x', either out of curiosity or not believing him.
- Ginko warns a person that the benefit they receive from a mushi is only temporary and will bite them in the ass eventually. The person is too attached to said benefit to let it go.
- Ginko warns a fellow Mushishi that they are doing something wrong and is ignored out of pride.
- Ginko warns a person but his strange appearance and status as an outsider generates distrust and he is ignored.
- Ginko warns a person but they don't believe him because they can't see or have never heard of mushi.
- Martial Pacifist: Ginko won't actively harm anyone or anything unless he has no other choice, and even then he tries to find another way.
- Mr. Exposition: In almost every episode, he explains to the Victim of the Week (and the audience) what the episode's resident mushi does and how best to deal with it.
- Mystical White Hair: His mop of unusual white hair was caused by the same mushi that stole his memories.
- Peek-a-Bangs: His haircut covers one eye. Or rather, the lack of one eye.
- Smoking Is Cool: He's always smoking a special kind of cigarette whose smoke repels mushi.
- The Stoic: Ginko almost never loses his cool, which make the rare moments when he does all the more effective.
- Supporting Protagonist: Is usually this to whoever the Woobie of the Week is, sometimes only having a couple minutes of screentime in an episode despite being the show's protagonist.
- Walking the Earth: Ginko is always on the move, as he attracts mushi with his presence, which would wreak havoc anywhere he might settle down.
- Weirdness Magnet: Bordering on Doom Magnet. Ginko attracts mushi just by existing, and has to constantly be moving. Were he to settle down anywhere, the place would soon be overrun by an infestation.
AdashinoThe resident doctor of a small fishing village and a good friend of Ginko's. His obsession with mushi, despite not being able to see them, and all items related to them tends to get him into trouble.
- Collector of the Strange: He collects items related to mushi, and frequently tries to get Ginko to sell him items from his own supplies.
- Friend to All Children: There's usually a small gang of children following him around whenever he's not seeing patients or hanging out with Ginko.
- High-Class Glass: His most distinctive feature is his monocle. It makes him look refined and, at times, sinister.
Tanyu KaribusaA scribe who is responsible for sealing away a destructive mushi by transferring it from her body to written scrolls. She's also a close friend to Ginko.
- Birthmark of Destiny: The mushi sealed away in her body manifested itself as a coal-black birthmark, identifying her as a scribe destined to continue eradicating the mushi curse plaguing her family for generations.
- I Just Want to Be Normal: She had this attitude as a child, not fully understanding why she had to spend so much time cooped indoors studying or why her leg was black and couldn't move.
Tama MinaiTanyu's caretaker and a former Mushishi.