Japanese Cultural and Martial Arts Academy
The same person compiled the ninja "bible" called the Bansenshukai used by both the Iga Ryu and Koga Ryu. If I use modern terminology, the name of the author in the Koga Ryu edition was Koyo Onshi Fujibayashi Sabuji Yasutake while the name of the Iga Ryu edition author was Inyo Onshi Fujibayashi Sabuji Yasutake, and hence the only difference is the "nickname" used by each ryu for the author of its' edition.
The Koga Ryu is referred to as Koga Goju Sanke (53 Koga Families) and the Iga Ryu is referred to as Iga Yonjuku Ryu (49 Iga styles). This means that each individual ninja lived at a different location with different administration while using the same language and performing the same job, one is referred to as Iga Ryu while the other is referred to as Koga Ryu.
In olden times, through political necessity, a large area was split into the regions of Iga and Koga. The reason that Iga and Koga separated was due to temple and aristocracy territorial land disputation. Under these circumstances the Koga Ryu served the governing aristocracy to maintain their position while maintaining their close contact with the free land of Iga. Koga belonged to Omi (Shiga prefecture), which was controlled directly by the authority of the aristocracy, whether Koga liked it, or not. The distinction between Iga Ryu and Koga Ryu first appeared during the Sengoku period (1467 - 1576 A.D.). The battle that the ninja of Iga and Koga are famous for is called "Magari no Jin", and this is the point in history when people started referring to Iga and Koga ninja separately.
There are two important relevant notations in the history of the Koga Ryu
Koga Ryu Ninjutsu learnt Heiho (ninjutsu, bujutsu, heigaku) in Handozan. Handozan was the location of shugendo (yamabushi training) of En no Gyoja Kaiki. The first shugendo location was Yoshino, and then Handozan was founded and later came Heizan. Until the establishment of the 49 Temples of Shingon Shugendo in Iga, Handozan was the only shugendo place located in the northern part of Iga, and influential people classed as Dogo (mainly Hattori blood relatives from Iga and Koga) trained here. Handozan, the seed of ninjutsu, was the dojo credited with transmitting the founding yamabushi heiho to Iga. This dojo was also Koga's Dogo heiho training location. The people of Iga (mainly northern Iga) learnt Heiho with the people of Koga at Handozan until the establishment of the 49 Temples of Shingon Shugendo by Kobo Daishi Kukai, founder of Koyasan Shingonshu. Members of the Hattori family lived in both the Iga and Koga areas and this created a strong bond between the people of these two regions. The Hattori family had the greatest influence in both areas as they had blood relatives living in both Iga and Koga.