Cyanobacteria, also known as blue-green (micro)algae, are able to sustain many types of chemical stress because of metabolic adaptations that allow them to survive and successfully compete in a variety of ecosystems, including polluted ones. As photoautotrophic bacteria, these microorganisms synthesize aromatic amino acids, which are precursors for a large variety of substances that contain aromatic ring(s) and that are naturally formed in the cells of these organisms. Hence, the transformation of aromatic secondary metabolites by cyanobacteria is the result of the possession of a suitable “enzymatic apparatus” to carry out the biosynthesis of these compounds according to cellular requirements. Another crucial aspect that should be evaluated using varied criteria is the response of cyanobacteria to the presence of extracellular aromatic compounds. Some aspects of the relationship between aromatic compounds and cyanobacteria such as the biosynthesis of aromatic compounds, the influence of aromatic compounds on these organisms and the fate of aromatic substances inside microalgal cells are presented in this paper. The search for this information has suggested that there is a lack of knowledge about the regulation of the biosynthesis of aromatic substances and about the transport of these compounds into cyanobacterial cells. These aspects are of pivotal importance with regard to the biotransformation of aromatic compounds and understanding them may be the goals of future research.