- Chikane was with the Orochi the whole time in the manga while in the anime she joined them after witnessing Himeko's first kiss.
- Himeko did not know who the Lunar Priestess was until halfway through the manga, at which point she was raped by Chikane, while in the anime, the priestesses worked together since the beginning.
- Makoto does not injure her leg in the manga from the attack on the school.
- Himeko does not respond to Chikane's death wish by injuring Chikane, but hugs and embraces her instead in the manga.
- Himeko, in the manga, stays on the moon with Chikane, and later both are reincarnated as twin sisters.
- In the manga, it is revealed that all the major players in the confrontation between Orochi and Ame No Murakumo, with the exception of Chikane, were brought to Mahoroba when Chikane's grandfather gathered together orphans from all over Japan in hopes that he would gather all the key players. For example, in the manga Himeko was not actually born in the village and was shipped in with a bunch of other orphans, while in the anime she is still an orphan but is not an "outsider".
- In the manga, the backgrounds, as in why they want to destroy everything, are not expanded upon, while the anime runs through each Orochi's motivations quickly later on in the series.
- In the manga, Makoto didn't take pictures of Himeko while she was dressing. Also, her symbol appears at the beginning of the series.
- There are a few diferences between characters appearance: Chikane has turquiose hair instead of dark blue and brown eyes insead of light blue eyes, Soma and Miyako have dark blue hair instead of black and respectively dark purple and Himeko's shade of blond is a pinky one in the manga