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Microscopic eukaryotes are important components of coastal wetland ecosystems. The goal of this study was to investigate the diversity of microeukaryotes in the tidal pools of a New Jersey salt marsh and to compare the assemblages of natural and artificial pools excavated for controlling mosquito populations. We evaluated microeukaryotic assemblages using the amplicon sequencing of 18S and rbcL DNA markers and the microscopic identification of diatoms in water and sediment samples. 18S unique amplicon sequence variants (ASV) representing ciliates, dinoflagellates, diatoms, and cercozoans were the most diverse, while the reads of dinoflagellates, diatoms, ciliates, and nematodes were the most abundant. The dominant ASVs were attributed to organisms that are characteristic of coastal plankton and sediments or those known for their resistance to salinity, desiccation, hypoxia, and UV stress. The sediment assemblages were more diverse compared to those from the water column and contained a larger portion of ASVs that were not assigned to any low-rank taxa, reflecting the current gaps in understanding the diversity of microeukaryotes. Most taxonomic groups were significantly different in their abundance and composition between natural and artificial pools. Dinoflagellates, haptophytes, chrysophytes, pelagophytes, and raphidophytes—the groups that include a large proportion of mixotrophic taxa and species known for forming harmful algal blooms—were more abundant in the artificial than in the natural pools. Fungi, labyrinthulomycetes, and peronosporomycetes were also more abundant in artificial pools, which may be related to organic matter enrichment. Diatoms and foraminifera showed an opposite trend of higher abundance in natural pools. [ABSTRACT FROM AUTHOR]