Synthesium pontoporiae, exclusive parasite of the endangered dolphin, Pontoporia blainvillei, is endemic and restricted to the South Atlantic and belongs to the Brachycladiidae family Odhner, 1905. The study of this family has been limited by the difficulty of accessing the parasites from their marine mammal hosts and as a consequence there is a paucity of genetic information available. Herein we present a genetic analysis using 18S rDNA sequences of S. pontoporiae and S. tursionis and the ND3 mtDNA sequence of S. pontoporiae. The genetic analysis of 18S rDNA sequences of brachycladiids and acanthocolpids determined two major clusters associated with their definitive hosts, marine mammals and fishes, respectively. Considering the tree topology of brachycladiids ND3 mtDNA gene, two clusters were defined, one with the Synthesium species. This work contributes with fundamental genetic information on S. pontoporiae, and suggests a Brachycladiidae genetic evolution related to their hosts.