In Feudal Japan, there were over 70 ninja ryu operating out of the Koga and Iga regions.  The Iga and Kōga clans have come to describe families living in the province of Iga (modern Mie Prefecture) and the adjacent region of Kōka (later written as Kōga), named after a village in what is now Shiga Prefecture. From these regions, villages devoted to the training of ninjas first appeared.  The remoteness and inaccessibility of the surrounding mountains may have had a role in the ninja's secretive development.  Historical documents regarding the ninja's origins in these mountainous regions are considered generally correct.  The chronicle Go Kagami Furoku writes, of the two clans' origins:

"There was a retainer of the family of Kawai Aki-no-kami of Iga, of pre-eminent skill in shinobi, and consequently for generations the name of people from Iga became established. Another tradition grew in Kōga".

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Iga-ryū (伊賀流) iterally means the "School of Iga” is a school of ninjutsu. It became one of the two most well-known ninja schools in Japan, along with the Kōga-ryū. The Iga-ryū originated in the Iga Province in the area around the towns of Iga and Ueno (modern Iga City in Mie Prefecture). 

Kōga-Ryū (甲賀流)  literally means the "School of Kōga"  is a school of ninjutsu. It originated from the region of Kōka (modern Kōka City in Shiga Prefecture).

Listed below are the ninja ryu that operated out of these regions.  This information comes from various Japanese historical text including the Bugei Ryuha Daijiten, this is one of the most comprehensive text of information about all Japanese Ryu-ha.