The chicken, which is the host for seven species of Eimeria, typically is infected simultaneously by multiple Eimeria species and the oocysts of coccidia are excreted in the feces. A prerequisite for investigation of individual Eimeria species is to isolate a single oocyst from fecal samples. A novel method for isolating a single Eimeria oocyst from poultry litter using a micromanipulator was developed. This simple method is fast and reliable, and provides direct isolation of a single sporulated oocyst from fecal samples harboring multiple Eimeria species or samples contaminated by other species of parasite.