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Abstract. Eastern boundary upwelling systems (EBUS) contribute a disproportionatefraction of the global fish catch relative to their size and are especiallysusceptible to global environmental change. Here we present the evolution ofcommunities over 50 d in an in situ mesocosm 6 km offshore of Callao, Peru, andin the nearby unenclosed coastal Pacific Ocean. The communities weremonitored using multi-marker environmental DNA (eDNA) metabarcoding and flowcytometry. DNA extracted from weekly water samples were subjected toamplicon sequencing for four genetic loci: (1) the V1–V2 region of the 16SrRNA gene for photosynthetic eukaryotes (via their chloroplasts) andbacteria; (2) the V9 region of the 18S rRNA gene for exploration ofeukaryotes but targeting phytoplankton; (3) cytochrome oxidase I (COI) forexploration of eukaryotic taxa but targeting invertebrates; and (4) the 12SrRNA gene, targeting vertebrates. The multi-marker approach showed adivergence of communities (from microbes to fish) between the mesocosm andthe unenclosed ocean. Together with the environmental information, thegenetic data furthered our mechanistic understanding of the processes thatare shaping EBUS communities in a changing ocean. The unenclosed oceanexperienced significant variability over the course of the 50 d experiment,with temporal shifts in community composition, but remained dominated byorganisms that are characteristic of high-nutrient upwelling conditions(e.g., diatoms, copepods, anchovies). A large directional change was found inthe mesocosm community. The mesocosm community that developed wascharacteristic of upwelling regions when upwelling relaxes and watersstratify (e.g., dinoflagellates, nanoflagellates). The selection ofdinoflagellates under the salinity-driven experimentally stratifiedconditions in the mesocosm, as well as the warm conditions brought about bythe coastal El Niño, may be an indication of how EBUS will respond underthe global environmental changes (i.e., increases in surface temperature andfreshwater input, leading to increased stratification) forecast by the IPCC.