Phytomyxea (plasmodiophorids) is an enigmatic group of obligate biotrophic parasites. Most of the known 41 species are associated with terrestrial and freshwater ecosystems. However, the potential of phytomyxean species to influence marine ecosystems either directly by causing diseases of their hosts or indirectly as vectors of viruses is enormous, although still unexplored. In all, 20% of the currently described phytomyxean species are parasites of some of the key primary producers in the ocean, such as seagrasses, brown algae and diatoms; however, information on their distribution, abundance and biodiversity is either incomplete or lacking. Phytomyxean species influence fitness by altering the metabolism and/or the reproductive success of their hosts. The resulting changes can (1) have an impact on the biodiversity within host populations, and (2) influence microbial food webs because of altered availability of nutrients (e.g. changed metabolic status of host, transfer of organic matter). Also, phytomyxean species may affect their host populations indirectly by transmitting viruses. The majority of the currently known single-stranded RNA marine viruses structurally resemble the viruses transmitted by phytomyxean species to crops in agricultural environments. Here, we explore possible ecological roles of these parasites in marine habitats; however, only the inclusion of Phytomyxea in marine biodiversity studies will allow estimation of the true impact of these species on global primary production in the oceans.