Nature is one of the most important sources of pharmacologically active compounds in the search for drugs against life threatening diseases. Even though plants and terrestrial microorganisms have played as an important source for the new drug candidates from nature, marine organisms such as tunicates, sponges, soft corals, sea horses, sea snakes, marine mollusks, seaweeds, nudibranches, sea slugs and marine microorganisms are increasingly attracting attention in recent years. Marine organisms also have the potential to develop into future drugs against important diseases, such as cancer, a range of bacterial and viral diseases, malaria, and inflammations. Even though the mechanism of action in the molecular level of most metabolites is still unclear, the mechanisms by which they interfere with the pathogenesis of a wide range of diseases have been reported. The knowledge of this is one of the key factors necessary to develop bioactive compounds into medicines. This is due to their structurally unique and pharmacologically active compounds. The potential pharmaceutical, medicinal and research applications of some of these compounds are discussed in hundreds of scientific papers, and are reviewed here.