Reliable historical sources from the time of Ninja amount to a few scattered accounts. Ninja were covert agents and mercenaries (active from approximately 1450 - 1650). They were primarily from the clans of Iga Province and Koga village. That's what we know.
Ninja grabbed the public imagination right from the start. They have been surrounded in myth and legend for over 500 years. Almost everything you've probably heard about Ninja is more myth than reality.
1. Ninja still existMost (reputable) historians agree that Ninja (Shinobi) were active from the 15th - 17th century. This was a time of great political instability in Japan (Warring States Period). Japan was unified by Tokugawa Ieyasu in 1603 and the Ninja faded away.
2. You can learn to be a NinjaNinja were a mystery even to their contemporaries. Historical accounts of Ninja are intriguing. They confirm that Ninja were skilled spies and guerrilla warfare specialists. Such documents speak little of Ninja training methodology. The Ninja were secretive.
A total of 8 modern schools of Ninjutsu (Ninja Martial Arts) claim to descend from Ninja traditions. Some claim to trace their linage back to the 12th century (hundreds of years before the Ninja first appeared).
Most Japanese martial arts experts and historians agree that the link between modern Ninjutsu and the historical Ninja is tenuous at best.
3. Ninja were heroes who fought the ShogunNinja were mercenaries for hire. Their number one customer was the Shogun.
One of the best historical records of Ninja is an account of the Shimabara Rebellion (1637–1638). It's considered the last record of real Ninja.
The Shogun and leader of Japan, Tokugawa Iemitsu hired 8 Ninja to help his Samurai defeat a Christian Rebellion. As the Christians made their last stand at Hara Castle — Ninja's scaled the walls of the castle at night with ease and sabotaged the Castle's defenses.
4. It was Ninja vs SamuraiIt's clear from historical records that Ninja were often from the Samurai warrior class.
Hattori Hanzo is perhaps the most famous Ninja. He was also a Samurai who saved the life of Tokugawa Ieyasu (the Shogun who unified Japan) and helped him come to power.
5. Ninja were a single groupThere were various clans of Ninja who had different espionage, sabotage, infiltration, and assassination methods. The best known ninja clans were the Iga and Koga. There were other clans who practiced shinobi (Ninja martial arts).
6. Mochizuki ChiyomeIf historical records of male Ninja are scarce — reliable historical records of female Ninja (Kunoichi) are even more rare.
The concept of Kunoichi originated with Edo-era tales of Mochizuki Chiyome. According to the story Mochizuki Chiyome was the wife of Mochizuki Nobumasa (a famous Samurai warlord). She was born into the Koga clan (a Ninja clan) and therefore had Ninja in her blood. Her husband asked her to organize an all female Ninja organization that became important to his military campaigns.
The earliest known records of all of this originated in Edo-era ukiyo-e publications. In the Edo-era printing methods were developed that allowed for cheap picture books to be published for the masses. Such publications are generally considered unreliable. They're the Edo-era equivalent of modern Japanese manga (comic books).
Many historians believe that Mochizuki Chiyome may be a legend.
7. Ninja invented Ninja Swords and Shuriken (Ninja Stars)Shuriken were widely used by Samurai and probably weren't invented by Ninja. There's also no evidence that Ninja developed their own swords.
Historians believed that Ninja used standard wakizashi or chokuto type swords of the period. The earliest known records of the stereotypical "Ninja sword" are from a 1962 Japanese Ninja movie entitled Shinobi no Mono. Amazingly replicas of these Ninja swords have made their way into Ninja museums in Japan.
8. Ninja EverywhereJapanese history is filled with spies, assassinations and tricky military tactics. Many such historical events are incorrectly attributed to Ninja.
(The 4th century prince Yamato Takeru disguised himself as a beautiful woman and assassinated two rival chiefs. He has often been called a Ninja despite the fact he predates Ninja by over 1000 years. Yamato Takeru is considered semi-legendary)