The seagrass Thalassia testudinum harbors a high specific richness of epiphytic algae due to its morphology and abundance on the coast of the Mexican Atlantic. Epiphytic algae are an important component because of its taxonomic composition and functional groups; additionally, they can be employed as bioindicators. The composition of epiphytic algae of a common forophyte was compared in two ecoregions: Santa Rosa, Quintana Roo with oligotrophic waters and Penacho del Indio, Veracruz with eutrophic waters. Larger coverage of foliate and filamentous algae was expected in the Penacho del Indio prairie due to its eutrophic nature. Seventy seven species of epiphytes were determined, 43 in Penacho del Indio and 46 in Santa Rosa. Overall, 17 species belonged to Cyanobacteria, 38 to Rhodophyta, 11 to Phaeophyceae and 11 to Chlorophyta. Chondria pygmaea, Myrionema magnusii, Hecatonema floridanum, Rosenvingea sanctae-crucis and 7 cyanobacteria represent new registers for the Atlantic coast of Mexico. Centroceras hyalacanthum and Myrionema strangulans are new records for Veracruz. The functional groups were represented by: 39 filamentous algae, 20 microalgae, 9 corticated macrophytes, 5 foliose algae, 3 crustose and one calcareous articulated macrophyte. Red algae displayed the highest specific richness at both sites, followed by green algae in Penacho del Indio and microalgae in Santa Rosa. Epiphytism of foliate, filamentous, as well as corticated macrophytes, had larger coverage and biomass in Penacho del Indio. The prominent development of Ulva at this locality supports its eutrophic condition, whereas epiphytes composition in Santa Rosa suggests the existence of oligotrophic waters.