Togakure Ryu Ninpo Taijutsu: 戸隠流忍法体術 (Hidden Door School) The second oldest of the nine traditions, this ryu forms much of the basis for the Ninjutsu techniques taught in the Bujinkan. This system is famous for its use of such weapons as shuko and shuriken. It was reportedly founded by Daisuke Togakure in the late 1100's.
Kumogakure Ryu Ninpo Taijutsu: 雲隠流忍法体術 (Hiding in the Clouds School) The second of the ninja ryus, it uses similar taijutsu as Togakure Ryu, and is also known for double blocks and strikes This ryu originated with Heinaizaemon Ienaga Iga in the mid 1500. Gyokushon Ryu Ninpo Taijutsu: 玉心流忍法体術 (Jewelled Heart School) The third ninjutsu ryu in the Bujinkan system was founded by Sasaki Goemon Teruyoshi in the mid 1500's. Not much is known of this ryu except that it is an Iga ninja school and concentrated more on the espionage side of ninjutsu, rather than the fighting side. It is also known for its use of sutemi (sacrifice) throws.
Shindenfudo Ryu Dakentaijutsu: 神伝不動流打拳体術 (Immovable Heart School) This system specializes in Dakentaijutsu (striking techniques), and jutaijutsu (hard grappling techniques). This was the first ryu that Takamatsu learned from his grandfather. This ryu was also founded by Izuma Kanja Yoshiteru in the mid 1100's who also learned Chinese kenpo.
Kukishinden Ryu Happo Bikenjutsu: 九鬼神伝流八法秘剣術 (Nine Demons School) This ryu is a battlefield style whose specialty is the use of many different weapons including spears, swords, hanbos, etc. Many of the weapon techniques (hanbo, bo, yari, naginata, etc) in Bujinkan come from this school. Kukishenden Ryu was reportedly founded by Izuma Kanja Yoshiteru in the mid 1100's.
Takagiyoshin Ryu Jutaijutsu: 高木揚心流柔体術 (High Tree, Raised Heart School) This system specializes in grappling and throwing techniques similar to aikido and judo. However, unlike judo and aikido, this style makes it difficult for the opponent to make ukemi (to fall or roll safely). This ryu is known as the "bodyguard school", and was founded by Takagi Oriuemon Shigenobu around 1650.
Gyokko Ryu Koshijutsu: 玉虎流骨指術 (Jeweled Tiger School) This style is heavily influenced by Chinese kenpo and is known for its koshijutsu attacks to muscles and soft organs, also using fingers and thumbs for ripping and tearing. Gyokko Ryu was originally founded by Cho Gyokko who was said to have fled China during the Tang Dynasty around 900 AD. This ryu forms much of the basis for the Bujinkan system including the kihon happo.
Koto Ryu Koppojutsu: 虎倒流骨法術 (Tiger Knocking Down School) This style specializes in koppojutsu or bone-breaking techniques and is very linear in motion. This style was originally organized into a ryu by Sakagami Kunishige in the mid 1500's. The name of the school means to knock the Tiger down with the tips of the fingers and historically, training started with striking sand and gravel, then larger stones for conditioning.
Gikan Ryu Koppojutsu: 義鑑流骨法術 (Truth Loyalty and Justice School) This ryu was originally founded by Uryu Hangan Gikanbo in the mid 1500's and specializes in koppojutsu or bone-breaking techniques. This style is known for its low stances, with much of the footwork within the Bujinkan system coming from this ryu.