During an epidemiologic survey following a mortality event of freshwater mussels in 2018 in the Embarrass River, Wisconsin, USA, we identified a novel microsporidian parasite in the ovary of mucket (Actinonaias ligamentina), plain pocketbook (Lampsilis cardium), and fatmucket (Lampsilis siliquoidea) (Unioinidae). Histopathology showed round-to-oval microsporidial spores in the cytoplasm of oocytes in 60% (3/5) of mucket, 100% (4/4) of plain pocketbook and 50% (1/2) of fatmucket. On transmission electron microscopy, mature spores were round to oval, measured 4.13 +/- 0.64 µm (3.14–5.31) long by 2.88 +/-0.37 µm (2.36–3.68) wide. Spores had a thin electron dense exospore with a spiky coat, a thick electron lucent endospore, diplokaryotic nuclei, a polar vacuole, and 27–28 polar filaments arranged in 1 to 3 rows. Sequencing of the small subunit rRNA produced a 1356 bp sequence most similar to Pseudonosema cristatellae, and phylogenetic analysis grouped it with freshwater Neopereziida. The morphologic and ultrastructural characteristics did not match those of Pseudonosema sp. and a new genus and species, Hirsutonosema embarrassi n. gen., n. sp., were designated. Additional studies could evaluate host susceptibility, distribution, seasonality, transmission, and lethal or sub-lethal effects of this parasite to freshwater mussels.