The Koga region of japan is well known for the ninja who came from there. It lies in what is now Shiga prefecture. It is a mountainous region surrounding Biwa Lake. The boundaries may have changed somewhat since the days of Feudal Japan but the region has changed less than you might think.
Though there are records going back as far as the Tenkyo era regarding the families there and some of the possible origins of ninjutsu in the region, it wasn't really until the end of the Nambuko era (1330's) that remnants of the Northern & Southern Imperial Courts fled, many to the Koga region and founded the actual Koga Ryu itself which eventually grew to 53 families. There are still many shrines, temples, castles and other structures that remain from the heyday of the ninja.
Shoro Enryakuji Temple
Daitsuji Temple
Hikone Castle
Hyakusai Temple Garden
Koga Ninja House
Some of the many famopus Shinobi family names from this region are Shinpi Ryu, Taira ryu, Isshu Ryu, Taro Ryu, kuriya Ryu, Tomo Ryu, Tatara Ryu, Otomo Ryu, Hiryu Ryu, Fujiwara Ryu, Sasaki Ryu, Byaku Ryu and Sugawara Ryu.