A previously unrecognized microsporidian (Kabatana newberryi n. sp.) is described from the musculature of Eucyclogobius newberryi (Gobiidae) in Big Lagoon, Humboldt County, California. Spores are ovoid, ranging in size from 2.8 ± 0.3 μm in total length and 1.9 ± 0.4 μm in width (measurements of 30 spores made by calculation from micrograph). The polar filament has 9–10 coils in 1–2 rows. Development occurs in direct contact with host muscle cell cytoplasm, without xenoma or sporophorous vesicle. Phylogenetic analysis of the new species and of 35 other microsporidians known to infect fish using 1,115 base pairs of aligned 16S rRNA gene indicate the new species is most closely related to Kabatana takedai. However, the new species differs by 11% sequence divergence from K. takedai. Divergence in morphology and genetic data allow for diagnosis from all other fish-infecting microsporidia and supports recognition of a new species of microsporidian, Kabatana newberryi n. sp., presently known only from a suspected specific host, the endangered tidewater goby Eucyclogobius newberryi.