One method was to take the fungi poison out of the blowfish or puffer fish. This poison is very strong and can kill in small doses. Another animal based poison was the bufo marinus. The bufo marinus is a large toad with an extremely toxic poison behind its eyes. This poison was often used on darts, arrows and spear tips.
Spiders and scorpions were also used. Not always just the poison extracted from them, but sometimes it was just as easy to slip a couple of scorpions in the bed of the victim.
One of the organic poisons used was made from common fruit. Cyanide was extracted from a variety of sources, such as apple seeds, plum seeds, cherries seeds and many more. It was readily available to the ninja and was used often.
Tomato and rhubarb leaves also held a poison. Eating the leaves cause cardiac problems, ultimately resulting in cardiac arrest.
The amanita phalloides is a deadly mushroom. The poison in the mushroom was 10 times more powerful than that of cyanide. Eating the mushroom was certain death, and it was easy to slip a piece of the mushroom in almost any meal.
The poison could be used in various ways, depending on the situation. For example, if the ninja could slip it into the victims food while its being prepared. Without knowing what kind of danger he was in, the victim would eat the food infested with the poison. Not all the poisons used by the ninja were fatal, some of them were used to merely paralyze or cause blindness. It was not always necessary to kill.
Another thing the ninja did was dip their weapons, such as the shuriken or their sword, in the poison. This was so when it punctured the skin of their target, the fast acting poison would take its course, causing much more devastating than the blade itself.