Seas and oceans offer a wide range of temperature, pressure, light and chemical conditions thus allowing a wide diversity of marine organisms from shallow coastal waters to the deep ocean. These resources can be used to obtain new products and develop services, and in turn help to provide solutions to the challenges that affect our planet, including offering a sustainable supply of food and energy, new industrial materials and processes, new bioactive compounds, and new health treatments. Marine compounds have been identified as having antibacterial, anticoagulant, antifungal, antimalarial, antiprotozoal, antituberculosis, and antiviral activities. The major sources of these bioactive compounds are marine sponges, coelenterates, and microorganisms, followed by algae, echinoderms, tunicates, molluscs, and bryozoans. The discovery of bioactive compounds from marine samples is a hot topic considering the current need for sustainable use of marine resources. This book is a comprehensive overview of the analytical techniques employed in the discovery and characterization of bioactive compounds isolated from (all possible) marine samples and gives future perspectives of analytical methodologies. This overview includes an assessment of the sampling and preparation of extracts, the separation and isolation of bioactive compounds, their structural characterization and the application of bioassays in the discovery of bioactive compounds.