Just how does one assess ecosystem health? This has been a contentious topic with much debate in part because there are disagreements on the definitions of ecosystem and health. However, the question is particular topical for coral reefs. Coral reefs are known as the rainforests of the sea. They are among the most diverse ecosystems on earth providing habitat for fish and other invertebrates and income and storm surge protection for coastal communities. Unfortunately, coral reefs face many threats including coastal pollution, bleaching events associated with elevated ocean temperatures, ocean acidification that is impairing the ability of many marine organisms to deposit calcium, and overfishing that is altering trophic structures. Importantly, disease is playing an increasingly important role in decline of coral reefs. Over the last 40 years, we have done a good job documenting decline of corals, but we have few clues as to why these animals are dying or causes of diseases. This is unfortunate because knowing causes of disease allows one to formulate management option to mitigate their effects. Unlike terrestrial animals, investigations of disease and disease pathogenesis in tropical marine ecosystems pose their own particular challenges. A lot of the existing literature is not inspiring and so gives one little to go on for foundational knowledge. One approach to understanding ecosystem health is to look at the health of ecologically functional groups that span trophic levels. Examples will be shown here on the weird and wonderful stuff one finds when adopting this approach using organisms ranging from corals to sea turtles and a few critters in between. In some cases, this information has important management ramifications.