Novel bioactive compounds are in high demand due to the development of microbial antibiotic resistance, increase in age-related diseases, and requirements for optimized manufacturing processes. The bioactive compounds can act as specific antitumor, anti-inflammatory, and antifungal compounds as well as pharmaceuticals against metabolic diseases. Bioprospecting from marine microorganisms has a tremendous potential for the discovery of novel bioactive compounds as enzymes and complex secondary metabolites for industrial as well as for biotechnological and therapeutic applications. A bioprospecting process usually begins with the isolation of a native microorganism, extraction of compounds from a culture sample, or with the isolation of environmental DNA for either heterologous expression or sequencing. Extracts from live microorganisms can be screened for bioactivity in function-based screening assays, while DNA from either the isolated microorganisms or from the environment can be screened with sequence-based screening methods or genome mining. Once a desired activity has been detected, the bioactive compound should be purified, the structure should be elucidated, and preferably its mechanism of action should be described. In this chapter, we give an overview of the bioprospecting process with special focus on compounds with therapeutic properties from marine microorganisms, and we evaluate some of the most commonly used strategies that have been used at different steps in the bioprospecting processes when searching for novel bioactive compounds.