ABSTRACT Marinomyxa is a genus of obligate intracellular parasitic protists known to infect tropical seagrasses of the genus Halophila . The genus has attracted increasing attention since the rediscovery of Marinomyxa galls in the invasive seagrass Halophila stipulacea in the Eastern Mediterranean Basin in 2015, with numerous subsequent reports documenting its spread throughout the Mediterranean and Caribbean Seas alongside its host. To date, two species have been formally described: Marinomyxa halophilae , parasitising Halophila ovalis and Halophila major ; and Marinomyxa marina , infecting H. stipulacea . Here, we present molecular and morphological data on Marinomyxa infections in two additional Halophila species. We report galls in the cosmopolitan Halophila decipiens from Puerto Rico caused by M. halophilae , and in the vulnerable intertidal seagrass Halophila beccarii from southeast Asia caused by a previously undescribed parasite. Phylogenetic analyses based on 18S and 28S rRNA gene sequences reveal that the parasite found in tissues of H. beccarii represents a distinct lineage within the genus, which we designate as Marinomyxa denhartogi sp. nov. Through analysis of a previously published environmental sequencing dataset from New Caledonia, we provide additional evidence that the presence of Marinomyxa can be traced even in remote areas of its hosts' geographical range. Our findings indicate that Halophila and Marinomyxa are persistently co‐occurring symbionts with a tightly linked co‐evolutionary history, suggesting that additional host–parasite associations remain to be discovered through broader sampling of seagrass populations.