Marine microorganisms are a rich source of bioproducts that can be used in various biotechnological applications. Most marine species are subjected to several biotic and abiotic environmental factors, including grazing and disease exposure, as well as changes in temperature, salt levels, and nutrient availability. Consequently, marine microorganisms developed adaptation mechanisms, including the synthesis of secondary metabolites, allowing for their adaptability and survival over millions of years. One of the highly promising secondary metabolites are ultraviolet (UV)-absorbing Mycosporine-Like Amino Acids (MAAs) with absorption maximum within UVA and UVB range (310–360 nm). These small, water-soluble molecules are commonly present in a wide range of marine species and have shown promising bioactive properties, including anti-inflammatory, antioxidative and photoprotective activities. However, the biotechnological uses of these secondary metabolites have often been limited due to small quantities recovered from natural resources, variation in their quantities and limited success in heterologous expression systems. Modern omics techniques allow for a better understanding of the MAA biosynthesis and their regulatory processes. Commonly, MAA biosynthesis occurs via a four-enzyme pathway that includes enzymes dehydroquinate synthase, enzyme O-methyltransferase, adenosine triphosphate grab, and a nonribosomal peptide synthetase. However, significant genetic differences exist between species in the genes encoding enzymes involved in MAA synthesis, indicating additional complexity that has not yet been fully investigated. The use of genome-mining techniques has made it possible to identify genetic variations within biosynthetic gene clusters (BGCs), which has led to the discovery of novel chemicals from uncommon sources. Based on the existing omics data, including MAAs, this study investigates the application of modern genomics technologies for connecting BGCs and secondary metabolites and assesses the potential use of innovative genome-mining algorithms to reveal an obscure potential of marine microorganism for new bioproduct synthesis.