Mycosporine-like amino acids (MAAs) are a family of more than 20 compounds having absorption maxima between 310 and 362 nm. These compounds are well known for their UV-absorbing/screening role in various organisms and seem to have evolutionary significance. In the present investigation we tested four cyanobacteria, e.g., Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 6301, for their ability to synthesize MAA and conducted genomic and phylogenetic analysis to identify the possible set of genes that might be involved in the biosynthesis of these compounds. Out of the four investigated species, only A. variabilis PCC 7937 was able to synthesize MAA. Genome mining identified a combination of genes, YP_324358 (predicted DHQ synthase) and YP_324357 (O-methyltransferase), which were present only in A. variabilis PCC 7937 and missing in the other studied cyanobacteria. Phylogenetic analysis revealed that these two genes are transferred from a cyanobacterial donor to dinoflagellates and finally to metazoa by a lateral gene transfer event. All other cyanobacteria, which have these two genes, also had another copy of the DHQ synthase gene. The predicted protein structure for YP_324358 also suggested that this product is different from the chemically characterized DHQ synthase of Aspergillus nidulans contrary to the YP_324879, which was predicted to be similar to the DHQ synthase. The present study provides a first insight into the genes of cyanobacteria involved in MAA biosynthesis and thus widens the field of research for molecular, bioinformatics and phylogenetic analysis of these evolutionary and industrially important compounds. Based on the results we propose that YP_324358 and YP_324357 gene products are involved in the biosynthesis of the common core (deoxygadusol) of all MAAs.