In recent years, the use of brown seaweeds (Phaeophyceae) and especially Fucaceae, has increased for a variety of applications including food additives, nutraceuticals, cosmetics, and agriculture, mainly because most edible brown algae contain valuable bioactive compounds. However, the growing demand for some species, such as Ascophyllum nodosum , has become a major concern due to the risk of overharvesting. Along with this increasing demand, there is growing awareness of the intricate interactions between algal hosts and their microbiota. The Fucaceae are of particular interest in this regard, as several species exhibit specificity with regard to their associated endophytic fungi. Many of these associated microbes produce a wide range of bioactive compounds themselves and may contribute to well-known properties previously attributed to the host. For some compounds, an alternative to wild harvesting could be the production of molecules of interest by organic synthesis or by biotechnological production, e.g., in microbial cell factories incorporating selected members of the algal microbiota. This requires in-depth knowledge of the alga and its microbiota to recognize the origin and the synthesis pathways of these bioactive compounds. This review presents the current understanding of the Fucaceae and their associated microbiota as sources of chemical compounds intended for diverse applications.