The founder of Eishin Ryū; was Hayashizaki Jinsuke Minamoto no Shigenobu, who lived between 1546 and 1621 in present-day Kanagawa Prefecture. Many of the historical details of Hayashizaki's life are suspect, since, like most famous martial artists in Japan, his story has been widely fictionalized. It seems, however, apparent that he grew up during a time of constant warfare in Japan and was exposed to various sword-fighting methods from an early age. It is said that he went to Yamagata Prefecture to pray for guidance and receive divine inspiration for a new way of drawing the sword. However the circumstances came about, at some point he established his own style of swordsmanship, calling it Shinmei Musōo-ryū; "divinely inspired, unparalleled style."

Hayashizaki's iaido has had many names since then. It is considered the foundation for the two major styles of iaido practiced today: Eishin-ryū; and Muso Shinden-ryū. In each generation, a headmaster, or sōoke, has been appointed to guide the practice of the art, and each sōoke has had his own influence on the development of iaido. As an example, Musōo Jikiden Eishin-ryū; was originally developed for the tachi, a slightly longer and more deeply curved predecessor of the katana. Hasegawa Chikaranosuke Eishin, from whom the style's name is derived, adapted the style to the newly developed katana.

One of the most important sōoke in the system is the 17 sōoke, Oe Masamichi. A lot of political issues based on his actions have caused the split of many styles that all claim Eishin-ryū lineage, as well as the division between Muso Shinden-ryūu and Muso Jikiden Eishin-ryū. However, Oe-sōoke is the one who combined the teachings of Shimomura-ha and Tanimura-ha, and organized Muso Jikiden Eishin Ryū into the system into the seiza (shoden), tatehiza (chuden), and okuiai (okuden) waza sets we know today.