Basilisk: Kouga Ninpouchou was authored by Masaki Segawa based on the 1958 historical fantasy novel Kouga Ninpouchou by Futaro Yamada. The manga was published in Japan in 2003 and 2004 by Kodansha's Young Magazine Uppers magazine. It won the 2004 Kodansha Manga Award for general manga.
Segawa used real images for the manga's backgrounds, superimposing his hand-drawn characters over them. Each chapter was named after the number of ninjas alive on each side.
The entire manga was later produced into five volumes. They were translated by Del Ray Manga for release in the U.S and Canada, and by Tanoshimi in the UK. It was also released in Germany with a German translation.