New World flying squirrels, Glaucomys spp., are nocturnal arboreal sciurid rodents that have been previously surveyed for coccidial parasites. To date, 4 species of Eimeria have been reported from 2 species of Glaucomys. Here we report 2 species of eimerians from southern flying squirrels (Glaucomys volans) and the endemic Prince of Wales flying squirrel (Glaucomys sabrinus griseifrons). Oocysts of Eimeria dorneyi Levine and Ivens were found to be passing in the feces of 4 G. s. griseifrons from Alaska and a new species of Eimeria was present in feces from 6 G. volans from Arkansas. Oocysts of Eimeria hnidai n. sp. are ellipsoidal with a bilayered wall, measure 23.7 × 13.7 μm, and have a length/width (L/W) ratio of 1.7; a micropyle and oocyst residuum are absent but polar granule(s) are present. Sporocysts are ellipsoidal–elongate and measure 11.8 × 4.9 μm, L/W 2.2; Stieda body is present but sub-Stieda and para-Stieda bodies are absent. The sporocyst residuum is composed of small indistinct granules along the edge or in the center of the sporocyst. This is the first coccidian reported from G. volans from Arkansas as well as the initial coccidian (E. dorneyi) reported from G. s. griseifrons from Alaska. We also provide a summation of the coccidia known from North American flying squirrels.