Hypoxia often causes the large-scale mortality of benthic organisms and alters the structure and function of pelagic and benthic communities. Protists are a major component of pelagic and benthic communities. Using a metabarcoding analysis, we explored the temporal changes in the structure of protist communities incubated for seven days under normoxic (7.0 mg L-1) and hypoxic (1.5 mg L-1) conditions. The incubated water was originally collected from Tongyeong Bay, Korea, where hypoxia frequently occurs. Among the phyla, the relative amplicon sequence variant (ASV) abundance of Cercozoa and Ochrophyta increased under hypoxia from day 0 to day 7, whereas that of other phyla declined or remained similar. Moreover, the relative ASV abundances in the phylum Dinoflagellata under both oxygen conditions were highest on days 0, 3, and 7. Among the dinoflagellate orders, the highest dinoflagellate ASV abundance under hypoxia on day 7 belonged to the order Peridiniales, whereas the highest relative read abundance belonged to Prorocentrales. The 35 dinoflagellate species that were detected under the hypoxic condition during incubation were autotrophic (two), phototrophic (autotrophic or mixotrophic) (15), mixotrophic (eight), kleptoplastidic (one), heterotrophic (eight), and parasitic (one), indicating that dinoflagellates with diverse trophic modes are present under hypoxia. Of these detected dinoflagellate species, 14 were present under the hypoxia on day 7. Furthermore, 19 dinoflagellate species were newly determined to be present under hypoxia, 6 of which were present on day 7. These findings highlight the ecological resilience and adaptability of protist communities under the hypoxic condition. The present study provides insights into the potential roles of protists in maintaining ecosystem functions in the oxygen-depleted environments.