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It was during the Southern Sung period that Dogen Zenji traveled to China to study the Dharma. After visiting many temples there, Dogen Zenji, at the age of 26, encountered Nyojo Zenji, the abbot of Tendosan Keitokuji and the dharma heir of the Soto Zen lineage. Because of this fortunate meeting, Dogen Zenji was able to study with Nyojo Zenji and succeed to the Authentically Transmitted Buddha Dharma that has been passed down from Shakyamuni Buddha.

Immediately after returning to Japan at the age of 28, Dogen Zenji authored A Universal Recommendation of Zazen (Fukan Zazengi) to proclaim the Authentically Transmitted Buddha Dharma. In spite of opposition from older schools of Japanese Buddhism, especially the monks on Mt. Hiei, Dogen Zenji felt it to be an urgent task to foster true seekers of the way in order to proclaim the truly transmitted teachings. With this in mind he first settled at Koshoji in Uji and then at Eiheiji in Echizen. Faithful to his pledge that even one person or even half a person would be enough, he dedicated himself wholeheartedly to raising up true followers of the Buddha Way.

This mind of Dogen Zenji was then passed on to his successors: Koun Ejo Zenji, the second abbot of Daihonzan Eiheiji, and from Ejo Zenji, Tettsu Gikai Zenji who founded Daijoji in Kaga. Tettsu Gikai Zenji’s disciple Keizan Zenji then inherited that Dharma. Among Keizan Zenji's disciples was Meiho Sotetsu Zenji who later inherited Yokoji, and Gasan Joseki Zenji who inherited Daihonzan Sojiji. These masters also produced many outstanding students who spread the teachings of the Soto Zen School around Japan.

Although the Rinzai Zen School, which also inherited one stream of Chinese Zen, had the support and belief of many powerful people, including the shogunate government and the nobility, the Soto Zen School counted adherents mainly among wealthy families in the rural districts as well as the general masses. Because of this the Soto Zen School popularized its teachings mainly in the countryside.

During the end of the Kamakura Period and into the Muromachi Period, the Rinzai Zen School established five main temples in Kyoto and Kamakura, thus inaugurating the system of the "Five Mountains-Ten Temples" (Gozan-Jissetsu). This greatly encouraged the development of culture influenced by the Zen mind, especially in the literary movement known as Literature of the Five Mountains (Gozan-Bungaku). In contrast, the Soto Zen School avoided connections with central power, preferring to merge with the masses and respond to the simpler needs of commoners while continuing a slow but steady course of teaching activities. Of course through the flow of history the Soto Zen School has experienced periods of confusion and change.

The establishment of the jidan seido (temple/lay parishioner's system) by the Shogunate in the Tokugawa Period led to central organization and control of temples throughout the country. During this time many outstanding masters teaching in the Soto Zen School made their appearance. They included Gesshu Soko, Manzan Dohaku and Menzan Zuiho. These masters were instrumental in correcting vices in Dharma transmission while emphasizing the need to return to Dogen Zenji's original mindfulness of Authentic Face-to-Face Transmission (menju-shiho). This was one part of a movement to revive the original realization of the Soto Zen School. It also led to copious research and editing of classics of the Soto Zen School, beginning with Dogen Zenji's magnum opus The Treasury of the True Dharma Eye (Shobogenzo).

With the Meiji Restoration, the new government rested on the authority of the Emperor and his divinity as it was supported by Shinto theology. Because of the close relationship between the emperor system and indigenous religion the government moved to locate the traditional Shinto religion in the center of society, separating Shinto and Buddhism while attempting to stamp out Buddhism. The government went so far as to proclaim the need to anti-Buddhist persecution (haibutsu-kishaku). This proved to be a major blow to the Buddhist world, but the various schools of Buddhism were able to overcome those troubles.

In this period the Soto Zen School saw the appearance of Ouchi Seiran Koji, who edited the original version of the Meaning of Practice and Verification (Shushogi). Azegami Baisen Zenji of Daihonzan Sojiji and Takiya Takushu Zenji of Daihonzan Eiheiji made revisions of Ouchi’s text and promulgated it as the standard for spreading the teaching of the Soto Zen School. The Shushogi has played a major role in popularization of the teaching among laypeople. Today, the Soto Zen School has developed into a major religious movement which includes about 15,000 temples and some eight million adherents throughout Japan.

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