The First Ninja Schools:
For over 100 years, the amazing meld of Chinese and Japanese fighting tactics that would later become ninjutsu developed. Basically, these methods grew as a counter-culture, and had no rules or regulations of any kind. Ninjutsu, as it was eventually known, was initially formalized by Daisuke Togakure and Kain Doshi.
Daisuke had been a Samurai, but he was stripped of his lands and his Samurai title when he was on the losing side of a battle. In 1162, while Daisuke was wandering the mountains of Japan, he encountered Kain Doshi, who was a Chinese warrior monk. Daisuke renounced his bushido code---the samurai code which means "Way of the warrior"---and the two teamed up to develop a new theory of guerrilla warfare called ninjutsu.
Daisuke's descendants went on to create the first ninja ryu, or school, called the Togakureryu.
To understand the difference between Ninja, or ninjutsu; and the Samurai, you must consider bushido, the samurai code of honor. To a Samurai, honor and loyalty were above everything else. When a Samurai went into battle, he selected one single opponent, announced his challenge, listed his family pedigree, and then attacked. All Samurai wore bright colors on their fighting armor that identified their clan.
The code of bushido practiced by the Samurai was definitely noble, but it simply didn’t get the job done in certain situations. That was where ninjutsu came in. According to the Ninja code, winning---or an accomplished mission---was valued above all else. This meant succeeding in the mission by whatever means were necessary, be it sneak attacks, poison, seduction, spying, etc. All of these tactics were shameful to the Samurai, but fair play by the Ninja’s code. Ninja's used many weapons, like the Sai, and throwing knives.