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Shoguns were the leaders, the ones who had all the power but he still didn't own most of he land. he was the one making all the decisions and he was second from the top of the feudal system.
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The emperors were at the top of the system, they ruled the land. Even though they were the most respected and feared figures in Japan, he had virtually no power, the shoguns had it. The emperor was more like the person that overlooks things, even though if he didn't like something, he couldn't do anything about it.