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Ninjutsu's roots are going deep into Japan's history, and are directly related to its warriors history, clans fight, social segregation and military conditions. Many of the Ninjutsu schools were founded by formal samurais, willing to follow a different path, with a different understanding of the man, nature and fight techniques relation. With influences coming from the continent (chinese military, warrior monks, political refugees), from China or Coreea, the first art's methods were created as a new concept of life, including religious practices, mind and body fortification techniques, nature understanding methods, and more.
This new concept was thought and practiced in several small warrior villages in the ancient Japanese Iga and Koga regions, in 11th and 12th centuries (though most of the Ninjutsu schools were codified as we know them today later, in 15th century). With a self governing and a strong geographical position, the Iga and Koga regions became in the Kamakura period (1185-1333) well known for their warriors abilities, the historians identifying about 75 Ninjutsu families in Iga and approximate 53 families in Koga who were regularly employed by some of the Japan's leading casts. Organized in a hierarchical structure of jonin (high level ninja) chunin (middle level ninja) and genin (low level ninja), the ninja families/clans were variously sized from small family groups to large clans organized as small armies, very disciplined and relying on the military and political abilities of the clan's ruling casts.
Their military power and the success of some of their operations created such popularity and fear, and they became such a respectful military force (and possible allies), that the general Oda Nobunaga was determined to start the historical extermination campaign against Iga warriors villages, hoping to eradicate the warrior clans in 1581. Though Nobunaga succeed to overwhelm and defeat the Iga ninja warriors, the survivors spread in the other regions and kept practicing and transmitting through generations their art and knowledge.
The opposition between the believes and practices of Ninjas and Samurais was intensively used in either american or asian commercial cinematography, though on those times it was quite unappropriate to make a clear distinction between the warrior casts. They were all military trained, but it was the philosophical approach that made the difference. One of the remarkable historical situations was when Hanzo Hattori, a formal bushi who become a famous ninja warrior, and his people were actually hired as personal daimyo (later shogun) Tokugawa bodyguards, after they successfully assured his protection to one of his military actions. It was one of the moments when ninjas came into legitimacy, and this also shows the relativity of position and relations that ninjas and samurai names had at that time.
But, in opposition with the samurai's honorific code, the new Ninjutsu art valued the life and the survival more than the death in honor. The mean was not important as long as the goal was to be accomplished. With such beliefs, it is understandable why the ninjas were often secretly hired by different daimyo (japanese warlord) to accomplish necessary but desirable missions in their often military campaigns.
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After the Tokugawa shogunate, as the political and military situation became stable, ninja were effectively unemployed, ironically, the peace period being the most effective enemy for them. The knowledge was secretly transmitted within warrior families or clans through the centuries until today, when several of the ancient schools can be studied as part of the japanese history and culture.
Ninjutsu came back to light in the 70's, when Sensei Hatsumi founded Bujinkan as the first public and official Ninjutsu organization, and worked to made Ninjutsu seriously and correctly perceived by the society, by the other martial arts practitioners and by the non-japanese world. He accepted foreign (non-Japanese) students, and step by step, true Ninjutsu was spread around the world. Un unfortunate turn appeared when Ninjutsu became the subject of low quality & budget American films in the 70s - 80s, promoting an image of a mysterious, super-human, often devilish warrior; this happened because of both misunderstanding of Ninpo/Ninjutsu facts, and because of commercial attempts of a profitable growing consuming society. This made possible for a lot of martial arts practitioners with "enough initiative" to speculate this unapropriate image, and to take financial advantages of people willing to learn Ninjutsu, by creating "true ninjas" schools with black hoods and shurikens all over.
The effects of such a bad publicity are still supported today in general public opinion, ninja and Ninjutsu being often associated with assasins, super powered fantasy heroes, misterious religious or martial arts impostors. It comes as a natural responsability of the legitimate Ninpo/Ninjutsu organizations to promote the real and the true art as teach in Japan.
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