Chemical interactions have been shown to regulate several marine life processes, including selection of food sources, defense, behavior, predation, and mate recognition. These chemical communication signals have effects not only at the individual scale, but also at population and community levels. This review focuses on chemical interactions between marine fungi and microalgae, summarizing studies on compounds synthetized when they are cultured together. In the current study, we also highlight possible biotechnological outcomes of the synthetized metabolites, mainly for human health applications. In addition, we discuss applications for bio-flocculation and bioremediation. Finally, we point out the necessity of further investigating microalgae-fungi chemical interactions because it is a field still less explored compared to microalga–bacteria communication and, considering the promising results obtained until now, it is worthy of further research for scientific advancement in both ecology and biotechnology fields.