This project aimed to evaluate the ability to use metabarcoding for characterizing the harmful algae species present in known cultures or in samples taken from nature. The work was done using both metabarcoding with next-generation sequencing and with taxonomic identification by microscopy. Samples were additionally evaluated using known qPCR primers. The following amplicons were used: 16S, 18S dinoflagellate and 18S diatom, and large subunit (LSU) rDNA.