The coccidian parasite Cystoisospora canis (syn. Isospora canis) can cause clinical disease in dogs. Three generations of meronts are reported to occur in the small intestine of experimentally infected dogs before gametogony and oocyst formation. Oocyst excretion in the feces occurs at 9 to 11 days post-inoculation (PI). We examined the late asexual and sexual development of C. canis in 2 dogs necropsied 10 days after oral inoculation with 100,000 sporulated C. canis oocysts; both dogs had excreted oocysts 9 days PI. Asexual and sexual stages were seen in the lamina propria, throughout the small intestine in sections stained with hematoxylin and eosin from both dogs. In other studies of the C. canis life cycle, little attention has been given to distinguishing the last asexual generation of meronts and early microgamonts that can appear similar due to their stage of maturation and both having multiple nuclei. Here we report newly identified features of developing meronts and microgamonts and their distinction from each other by using sections processed using the periodic acid–Schiff (PAS) reaction. Using this method, we demonstrated that PAS-positive granules could be used to identify microgamonts and differentiate them from developing meront stages. These findings will aid pathologists and others in properly identifying coccidial parasites, in determining the cause of microscopic lesions in intestinal tissue, and in accurately identifying etiological agents.