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Testate (shell‐building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida‐specific primers for theSSU‐rDNAgene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36‐cm horizontal transects and vertical cores; and (2) 26‐m horizontal transects fractioned into four size classes (2–10, 10–35, 35–100, and 100–300 μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized byDNA(i.e. active + quiescent) are distinct from those characterized byRNA(i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life‐history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.