The establishment of the Zen school of Buddhism is traditionally attributed to Bodhidharma.
Bodhidharma's arrival in China is dated to the Liu Song Dynasty (420–479) in the Continued Biographies of Eminent Monks (645) and to 527• in the Anthology of the Patriarchal Hall (952). Though they agree on almost nothing else, all the forms of the Bodhidharma legend concur that he ultimately settled in the kingdom of Wei where he took as disciples Daoyu and Huike. In his "Notes on some artists of the Six Dynasties and the Tang," Paul Pelliot asserts that all accounts of Bodhidharma are legendary. The noted historian J. A. G. Roberts in his book The Complete History of China notes that Zen Buddhism most likely was an indigenous development within China.


Shortly before his death, Bodhidharma appointed his disciple Huike to succeed him, making Huike the first Chinese patriarch and the second patriarch of Zen in China. The transmission then passed to the second, third, and fourth patriarchs, of whom little is known beyond their names. The sixth and last patriarch, Huineng (638–713), was one of the giants of Zen history, and all surviving schools regard him as their ancestor. However, the dramatic story of Huineng's life tells that there was a controversy over his claim to the title of patriarch: after being chosen by Hongren, the fifth patriarch, he had to flee by night to Nanhua Temple in the south to avoid the wrath of Hongren's jealous senior disciples. In the middle of the 8th century, monks claiming to be the successors to Huineng, calling themselves the Southern school, cast themselves in opposition to those claiming to succeed Hongren's student Shenxiu (神秀). It was at this point—the debates between these rival factions—that Zen enters the realm of fully documented history. The Southern school eventually became predominant and their rivals died out.

In the following centuries, Zen grew to become the largest sect in Chinese Buddhism. The teachers claiming Huineng's posterity began to branch off into numerous different schools, each with their own special emphasis, but all of which kept the same basic focus on meditational practice, personal instruction and personal experience. During the late Tang and the Song periods, the tradition truly flowered, as a wide number of eminent teachers, such as Mazu (WG: Ma-tsu), Baizhang (Pai-chang; Japanese: Hyakujo), Huangbo (Huang-po; Japanese: Obaku), Linji (Lin-chi; Japanese: Rinzai), and Yunmen (Japanese: Ummon) developed specialized teaching methods, which would variously become characteristic of the five houses (五家) of mature Chinese Zen. The traditional five houses were Caodong (曹洞宗), Linji (臨濟宗), Guiyang (潙仰宗), Fayan (法眼宗), and Yunmen (雲門宗). This list does not include earlier schools such as the Hongzhou (洪州宗) of Mazu.

Over the course of Song Dynasty (960–1279), the Guiyang, Fayan, and Yunmen schools were gradually absorbed into the Linji. During the same period, the various developments of Zen teaching methods crystallized into a technique that was unique to Zen Buddhism: koan practice (described below). According to Miura and Sasaki, "it was during the lifetime of Yüan-wu's successor, Ta-hui Tsung-kao 大慧宗杲 (Daie Sōkō, 1089-1163) that Koan Zen entered its determinative stage." Koan practice was prevalent in the Linji school, to which Yuanwu and Ta-hui (pinyin: Dahui) belonged, but it was also employed on a more limited basis by the Caodong school. The teaching styles and words of the classical masters were collected in such important Zen texts as the Blue Cliff Record (1125) of Yuanwu and The Gateless Gate (1228) of Wumen, recording classic koan cases which would be studied by later generations of students down to the present.

Zen, which had developed into a distinctively Chinese school of Buddhism, became an international phenomenon early in its history. This first occurred in Vietnam, according to the traditional accounts of that country. These traditions state that, in 580, an Indian monk named Vinitaruci (Vietnamese: Tì-ni-đa-lưu-chi) travelled to Vietnam after completing his studies with Sengcan, the third patriarch of Chinese Zen. This, then, would be the first appearance of Vietnamese Zen, or Thien (thiền) Buddhism. The sect that Vinitaruci and his lone Vietnamese disciple founded would become known as the oldest branch of Thien. After a period of obscurity, the Vinitaruci School became one of the most influential Buddhist groups in Vietnam by the 10th century, particularly so under the patriarch Vạn-Hạnh (died 1018). Other early Vietnamese Zen schools included the Vo Ngon Thong (Vô Ngôn Thông), which was associated with the teaching of Mazu, and the Thao Duong (Thảo Đường), which incorporated nianfo chanting techniques; both were founded by Chinese monks. All three of the early schools appear to have largely disintegrated during the Mongol invasions of the 13th century. A new school was founded by one of Vietnam's religious kings; this was the Truc Lam (Trúc Lâm) school, which evinced a deep influence from Confucian and Taoist philosophy. Nevertheless, Truc Lam's prestige waned over the following centuries as Confucianism became dominant in the royal court. In the 17th century, a group of Chinese monks led by Nguyen Thieu (Nguyên Thiều) established a vigorous new school, the Lam Te (Lâm Tế), which is the Vietnamese pronunciation of Linji. A more domesticated offshoot of Lam Te, the Lieu Quan (Liễu Quán) school, was founded in the 18th century and has since been the predominant branch of Vietnamese Zen.

The Zen school began to appear in Korea in the 9th century. During his lifetime, Mazu had begun to attract students from Korea; by tradition, the first Korean to study Zen was named Peomnang. Mazu's successors had numerous Korean students, some of whom returned to Korea and established the Nine Mountain Schools. This was the beginning of Korean Zen, which is called Seon. Among the most notable Seon masters were Jinul (1158–1210), who established a reform movement and introduced koan practice to Korea, and Taego Bou (1301–1382), who studied in China with Linji teacher and returned to unite the Nine Mountain Schools. In modern Korea, by far the largest Buddhist denomination is the Jogye Order, which is essentially a Zen sect; the name Jogye is the Korean equivalent of Caoxi (曹溪), another name for Huineng.

Although the Japanese had known of Zen for centuries, it was not introduced as a separate school until the 12th century, when Myōan Eisai travelled to China and returned to establish a Linji lineage, which is known in Japan as Rinzai. Decades later, Nanpo Jomyo (南浦紹明) also studied Linji teachings in China before founding the Japanese Otokan lineage, the most influential branch of Rinzai. In 1215, Dogen, a younger contemporary of Eisai's, journeyed to China himself, where he became a disciple of the Caodong master Tiantong Rujing. After his return, Dogen established the Soto school, the Japanese branch of Caodong.

The Zen schools also continued to develop in China up to the present.

The schools of Zen that currently exist in Japan are the Soto (曹洞), Rinzai (臨済), and Obaku (黃檗). Of these, Soto is the largest and Obaku the smallest. Rinzai is itself divided into several subschools, including Myoshin-ji, Nanzen-ji, Tenryū-ji, Daitoku-ji, and Tofuku-ji.

The Rinzai and Soto schools were founded in the 13th century and shortly before. Obaku, on the other hand, was introduced in the 17th century by Ingen, a Chinese monk. Ingen had been a member of the Linji school, the Chinese equivalent of Rinzai, which had developed separately from the Japanese branch for hundreds of years. Thus, when Ingen journeyed to Japan following the fall of the Ming Dynasty to the Manchus, his teachings were seen as a separate school. The Obaku school was named for Mount Obaku (Chinese: Huangboshan), which had been Ingen's home in China.

Some contemporary Japanese Zen teachers, such as Daiun Harada and Shunryu Suzuki, have criticized Japanese Zen as being a formalized system of empty rituals in which very few Zen practitioners ever actually attain realization. They assert that almost all Japanese temples have become family businesses handed down from father to son, and the Zen priest's function has largely been reduced to officiating at funerals.

The Japanese Zen establishment—including the Soto sect, the major branches of Rinzai, and several renowned teachers— has been criticized for its involvement in Japanese militarism and nationalism during World War II and the preceding period. A notable work on this subject was Zen at War (1998) by Brian Victoria, an American-born Soto priest.
This openness has allowed non-Buddhists to practice Zen, especially outside of Asia, and even for the curious phenomenon of an emerging Christian Zen lineage, as well as one or two lines that call themselves "nonsectarian." With no official governing body, it's perhaps impossible to declare any authentic lineage "heretical." Some schools emphasize lineage and trace their line of teachers back to Japan, Korea, Vietnam or China; other schools do not.

Over the last fifty years, mainstream forms of Zen, led by teachers who trained in East Asia and by their successors, have begun to take root in the West. In North America, the Zen lineages derived from the Japanese Soto school are the most numerous type. Among these are the lineage of the San Francisco Zen Center, established by Shunryu Suzuki; the White Plum Asanga, founded by Hakuyu Taizan Maezumi; Big Mind founded by Dennis Genpo Merzel; the Ordinary Mind school, founded by Joko Beck, one of Maezumi's heirs; and the Katagiri lineage, founded by Dainin Katagiri, which has a significant presence in the Midwest. Note that both Taizan Maezumi and Dainin Katagiri served as priests at Zenshuji Soto Mission in the 1960's.

Taisen Deshimaru, a student of Kodo Sawaki, was a Soto Zen priest from Japan who taught in France. The International Zen Association, which he founded, remains influential. The American Zen Association, headquartered at the New Orleans Zen Temple, is one of the North American organizations practicing in the Deshimaru tradition.

The Sanbo Kyodan is a Japan-based reformist Zen group, founded in 1954 by Yasutani Hakuun, which has had a significant influence on Zen in the West. Sanbo Kyodan Zen is based primarily on the Soto tradition, but also incorporates Rinzai-style koan practice. Yasutani's approach to Zen first became prominent in the English-speaking world through Philip Kapleau's book The Three Pillars of Zen (1965), which was one of the first books to introduce Western audiences to Zen as a practice rather than simply a philosophy. Among the Zen groups in North America, Hawaii, Europe, and New Zealand which derive from Sanbo Kyodan are those associated with Kapleau, Robert Aitken, and John Tarrant.

There are also a number of Rinzai Zen centers in the West, such as the Rinzaiji lineage of Kyozan Joshu Sasaki and the Dai Bosatsu lineage established by Eido Shimano.

Not all the successful Zen teachers in the West have been from Japanese traditions. There have also been teachers of Chan, Seon, and Thien Buddhism.

The first Chinese Buddhist priest to teach Westerners in North America was Hsuan Hua, who taught Zen, Chinese Pure Land, Tiantai, Vinaya, and Vajrayana Buddhism in San Francisco during the early 1960s. He went on to found the City Of Ten Thousand Buddhas, a monastery and retreat center located on a 237 acre (959,000 m²) property near Ukiah, California. Another Chinese Zen teacher with a Western following is Sheng-yen, a master trained in both the Caodong and Linji schools (equivalent to the Japanese Soto and Rinzai, respectively). He first visited the United States in 1978 under the sponsorship of the Buddhist Association of the United States, and, in 1980, founded the Ch’an Mediation Society in Queens, New York.*.

The most prominent Korean Zen teacher in the West was Seung Sahn. Seung Sahn founded the Providence Zen Center in Providence, Rhode Island; this was to become the headquarters of the Kwan Um School of Zen, a large international network of affiliated Zen centers.

Two notable Vietnamese Zen teachers have been influential in Western countries: Thich Thien-An and Thich Nhat Hanh. Thich Thien-An came to America in 1966 as a visiting professor at UCLA and taught traditional Thien meditation. Thich Nhat Hanh was a monk in Vietnam during the Vietnam War, during which he was a peace activist. In response to these activities, he was nominated for the Nobel Peace Prize in 1967 by Martin Luther King, Jr. In 1966, he left Vietnam in exile and now resides at Plum Village, a monastery in France. He has written more than one hundred books about Buddhism, which have made him one of the very few most prominent Buddhist authors among the general readership in the West. In his books and talks, Thich Nhat Hanh emphasizes mindfulness (sati) as the most important practice in daily life.