In nature, organisms have developed different mitigation strategies to protect from
harmful UV radiation. Â Mycosporine-like amino acids (MAAs) are small molecules with robust ultraviolet (UV)-absorbing capacities and a huge potential to be used as an environmentally friendly natural sunscreen. MAAs, temperature, and light-stable compounds demonstrate powerful photoprotective capacities and the ability to capture light in the UV-A and UV-B ranges without the production of damaging free radicals. The biotechnological uses of these secondary metabolites have often been limited by the small quantities restored from natural resources, variation in MAA expression profiles, and limited success in heterologous expression systems. Overcoming these obstacles requires a better understanding of MAA biosynthesis and its regulatory processes. MAAs are produced via a four-enzyme pathway, including genes encoding enzymes: dehydroquinate synthase, enzyme O-methyltransferase, adenosine triphosphate grasp, and a nonribosomal peptide synthetase. However, there are substantial genetic discrepancies in the MAA genetic pathway in different species, suggesting further complexity of this pathway that is yet to be fully explored. In recent years, the application of genome-mining approaches allowed the identification of biosynthetic gene clusters (BGCs), which resulted in the discovery of many new compounds from unconventional sources. This research explores using genomic tools for linking BGCs and secondary metabolite production in protists. Specifically, we discuss using novel genome-mining tools to reveal a cryptic potential for MAA synthesis and how the genetic diversity of MAA biosynthetic pathways may influence MAA production.