There is also a third lineage in Japan called the Obaku sect. The Obaku sect traces its roots to the Lin-chi sect of the Ming dynasty. Because the Lin-chi sect changed somewhat during the centuries between the Northern Sung and Ming dynasties, the Rinzai and Obaku sects have different characteristics and styles. The Obaku sect still exists, but it is small, with only one temple remaining in Japan.

To make matters even more complex, there are two major branches of the Japanese Rinzai sect. One school was transmitted from China during the Northern Sung dynasty. Its headquarters is the Myo Shin Ji temple in Kyoto, from which stem many minor branches. The other major branch of the Rinzai sect was transmitted from China during the final years of the Southern Sung dynasty (1127-1279). This Zen school is situated in Enga Ku Ji temple in Kamakura, Tokyo.