Filarial parasites are members of the Phylum Nemata that comprise several species of medical and veterinary importance. Among the human diseases caused by members of this group of nematodes are river blindness and lymphatic filariasis, which afflict millions of people in the tropics. These diseases not only have an impact on the health of the people affected but also bear a great socioeconomic burden. Despite their relevance, the systematics of the filarial parasites is not well understood yet, and additional molecular phylogenetic studies are required to comprehend the evolution of these parasites. Identifying the patterns of evolution of these parasites will be of relevance in preventing emerging zoonoses. The present review examines the information about the molecular systematics of filarial parasites available in the literature and evaluates the relevance of the different directions of future research. Furthermore, it is also intended to highlight the relevance of molecular systematic studies in the molecular epidemiology research area.