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Coral reefs are typical ecosystems with underwater beauty. In addition to beauty, there is a function to reduce abrasion, marine biota residence and as well as educational facilities. The current state of coral reef ecosystems in Indonesia is quite alarming, the condition of coral reefs that are in very good condition is 6.39%, good condition is 23.40%, sufficient condition is 35.06% and bad condition is 35.15%. So there needs to be special handling to deal with these damage by using technological developments. Based on these conditions many researches emerged for observation and conservation. One of them is research on the development of conservation aids, the floating of these tools is accompanied by the development of increasingly natural ways of user interaction and tools. Natural interaction is characterized by interactions that transform human movements into direct digital action. Motion Tracking (MT) is one of the implementations of markerless/natural interaction, in which to identify projects is no longer based on certain symbols. MT reads body parts then converted into digital movements. This study aims to develop Real-Time Motion Autonomous Surface Vehicle (ASV) Controlling for Coral Reef Conservation and Fisheries using Fuzzy Algorithms. The tools produced by the study are controlled naturally, so it is expected to facilitate users in operating ASV. This tool is expected to facilitate monitoring and observation for the conservation of marine ecosystems (coral reefs and fisheries).