User blog comment:AssassinRome/Assassins in Japan?/@comment-1178891-20120806121309/@comment-13038232-20120806134007

Now that's a simple difference.
 * Assassins: Fighting against Templars for freedom and peace by assassinating important personalities allied with them.
 * Ninjas: Mercenaries hired to assassinate for a respective sum of money or valuable reward. Acting like the hitmen of Japan.