The genus of benthic dinoflagellates Ostreopsis is of particular interest because some species negatively impact human health and coastal marine ecosystems. Ostreopsis populations from a remote area, such as the Galapagos Marine Reserve with its unique biodiversity, can provide significant data. Samples of epibionthic dinoflagellates were collected from two islands (Santa Cruz and Santa Fé) in 2017. Species of the genera Gambierdiscus, Amphidinium, Coolia and Ostreopsis were found. Ostreopsis strains were isolated to characterize their morphology, molecular biology and toxicity. Three different morphotypes of Ostreopsis based on dorsoventral and width diameters (n=369) were distinguished. The small cell morphotype was dominant in ten samples, with abundances of up to 33405 cells g-1 fresh weight of macroalgae. A total of 16 strains were isolated from field samples with subsequent polymerase chain reaction amplifications of rDNA, 5.8S rDNA and internal transcribed space regions; 13 strains (small cell morphotype) clustered in the O. cf. ovata Atlantic/Indian/Pacific clade; and 3 strains (large cell morphotype) clustered in the Ostreopsis lenticularis genotype from the type locality. The strains proved to be non-toxic. The presence of these genera/species represents a potential threat to marine ecosystems, and it is thus important to consider benthic species in the surveillance of harmful algae blooms in the reserve.