AbstractOur study focuses on bacterial communities associated with two benthic, epiphytic dinoflagellates, Gambierdiscus australes and Ostreopsis cf. ovata, isolated from coastal waters of Las Palmas, Gran Canaria, and grown in clonal cultures. The goal was to characterize the stable bacterial consortia found within the phycosphere of each dinoflagellate species and establish into which functional group they fell. High‐throughput sequencing (HTS) results highlighted a higher bacterial diversity in O. ovata compared with G. australes. Alphaproteobacteria dominated in both dinoflagellates with Marivita and Labrenzia as the most represented OTUs in Ostreopsis and Gambierdiscus, respectively, and Thalassospira and Oceanicaulis well represented in both species. Based on SIMPER analyses, Labrenzia and the Phycispherales SM1A02, dominant in Gambierdiscus and Ostreopsis, respectively, accounted for the most significant difference between the two microbiomes. The microbiomes described here differed from those described for the same dinoflagellate species in other studies, which could depend on differences in environmental conditions, macroalgal substrate, and/or growth stage or bloom phase of the microalgal hosts. The distinct bacterial communities associated with the two potentially toxic dinoflagellates, isolated from the same site and sampling event and cultivated under the same conditions, suggest different modalities of interaction and interexchange between bacteria and their hosts.