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Foraminifera include diverse shell‐building lineages found in a wide array of aquatic habitats from the deep‐sea to intertidal zones to brackish and freshwater ecosystems. Recent estimates of morphological and molecular foraminifera diversity have increased the knowledge of foraminiferal diversity, which is critical as these lineages are used as bioindicators of past and present environmental perturbation. However, a comparative analysis of foraminiferal biodiversity between their major habitats (freshwater, brackish, intertidal, and marine) is underexplored, particularly using molecular tools. Here, we present a metabarcoding survey of foraminiferal diversity across different ecosystems using newly designed foraminifera‐specific primers that target the hypervariable regions of the foraminifera SSU‐rRNA gene (~250–300 bp long). We tested these primer sets on four foraminifera species and then across several environments: the intertidal zone, coastal ecosystems, and freshwater vernal pools. We retrieved 655 operational taxonomic units (OTUs); the majority of which are undetermined taxa that have no closely matching sequences in the reference database. Furthermore, we identified 163 OTUs with distinct habitat preferences. Most of the observed OTUs belonged to lineages of single‐chambered foraminifera, including poorly explored freshwater foraminifera which encompass a clade of Reticulomyxa‐like forms. Our pilot study provides the community with an additional set of newly designed and taxon‐specific primers to elucidate foraminiferal diversity across different habitats. [ABSTRACT FROM AUTHOR]