The first time
that the existence of the ninjas was known is back in 1487 when a small
group of ninjas fought with the feudal lords around the area today known
as the Shiga prefecture, against the troops of Ashikaga Yoshihiki, the 9th
Shogun of Muromachi.
At that time the local feudal lords where fighting to expand their territories,
this period is known as Sengoku Jidai (Period of the Warring States). Ninjas
played an important role during those years mainly but not only, collecting
information for the military commanders. In 1581, Oda Nobunaga in his struggle
to unify the country ordered a massive attack in the Iga Region where villages
were destroyed and entire families of ninjas killed.
With the prolonged period of peace under the Tokugawa's shogunate (1600~),
the number of active ninjas kept decreasing.
Some were employed by the Shogunate as guards and spies.
The last historical record is a group of 10 ninjas helped the shogunate
army during the ‘Revolt of Shimabara' (Nagasaki Pref.) in 1637 where more
then 30,000 followers of the Christian religion insured against the shogunate.
One of the most important script about Iga and Koga Ninjustu, the BansenShukai
(Ten Thousand Rivers Gather into the Sea) was written in 1676.
With no more enemies to fight, perfecting tactics and techniques became
more and more difficult, and NinJutsu started to fade away. 
GM Yunoki
and R.Turolla on the gravestone of Fujibayashi Y.
who compiled the Bansenshukai in 1676