Diagnosis can be difficult due to the lack of recognizable oocysts in the feces. PCR-based DNA tests and acid-fast staining can help with identification. The infection is often treated with trimethaprine-sulfamethaxozol [Bactrim, co-trimoxazole], because traditional anti-protozoal drugs are not sufficient. To prevent transmission, food should be cooked thoroughly and drinking water from streams should be avoided while outdoors.

There is no vaccine to control "Cyclospora" infection in humans at present, but one is available for reduction of fetal losses in sheep.