Microbial communities, associated with terrestrial mosses (Bryopsida) and the rhizosphere of agricultural and natural occurring seed plants, have been rather extensively examined; but less is known about associations with seedless vascular plants, including ferns. The New York fern (Thelypteris noveboracensis), typically found within deciduous forests, occurs in locally extensive stands in North America extending from northeastern Canada to southeastern U.S.A. Soil samples were obtained in autumn (2007) and early summer (2008) within a plot of T. noveboracensis in the understory of deciduous trees in the forest reserve at Torrey Cliff, NY to document the rhizosphere (root-associated) density of commonly occurring heterotrophic eukaryotic microbes (protozoa), including microflagellates, naked amoebae and testate amoebae. The ranges in densities (number/g soil dry weight) are as follows: microflagellates (6.5 × 10⁶–1.3 × 10⁸), naked amoebae (1.8 × 10³–4.0 × 10⁶) and testate amoebae (ca. 400). Very few active ciliates were observed. This is the first report of microbial communities associated with the rhizosphere of ferns and provides a step toward a more complete documentation of protozoa associated with plant communities. Some comparative data of protozoa associated with mosses and seed plants are also presented.