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The image of the ninja wearing all black is a popular one indeed, but there is really no evidence that ninjas ever wore such a costume. In fact, it is much more likely that ninjas dressed as regular civilians, which would have been far more effective camouflage in most situations than an all black suit. The use of disguises amongst ninja is common and well-documented. Ninja often dressed as monks, entertainers, fortune-tellers, merchants, or farmers. Each of these disguises carried advantages that dressing in all black did not. Dressed as monks, ninjas could conceal weapons in their robes. Dressed as entertainers, they could spy in enemy buildings without arousing suspicion. Dressed as fortune-tellers, they could extract information from unknowing targets. Dressed as merchants, they could travel freely across enemy borders. And while dressed as farmers, ninja carried simple gardening tools (such as sickles or trowels) and used them as deadly weaponry. In this way if a ninja were caught by authorities, he could claim that his deadly apparatus were tools, not weapons. Though they may not have been wearing all black stealth suits, ninjas were always well-disguised.
Ninjas probably did not actually wear black suits as they are popularly depicted. It is likely that they wore more advantageous disguises such as farmer, fortune-teller, merchant, or monk.