The classification of living organisms has modified numerous times, because some groups have been difficult to catalog. Currently, seven kingdoms are recognized: Animalia, Plantea, Protozoa, Fungi, Archaea, Bacteria and Chromista. The latter is a polyphiletic group, very morphologically variable, important in marine ecosystems. Molecular phylogeny allow classification according to kinship relationships. In this study, the ITS region was analyzed to verify the relationships between different edges of the Chromista kingdom. 46 DNA sequences of different species from the databases were selected, processed, and analyzed using bioinformatic methods of distance and phylogeny. All dendrograms showed a distribution of species according to the current classification, showing that the Chromistas form a different lineage of the Protozoa. Finally, more studies are needed to better decipher evolution, physiology, and ecology; and thus, develop conservation, management and biotechnology strategies.