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This work presents a technique for the autonomous segmentation and classification of coral through the combination of visual and acoustic data. Autonomous Underwater Vehicles (AUVs) facilitate the live capture of multi-modal sensor information about coral reefs. Environmental monitoring of these reefs can be aided though the autonomous extraction and identification of certain coral species of interest. The technique presented employs a two phase procedure of segmentation and classification to gather statistics about coral density during autonomous missions with an AUV.