Both Cyclospora and Cryptosporidium are intestinal Apicomplexan protozoa, and both of them cause diarrhea; they differ in infective stage(oocyst) morphology and shedding and other characteristic features.
Cyclospora oocysts (8-10µm) are slightly bigger than Cryptosporidium (4-6µm). A sporulated Cyclospora oocyst contains 2 sporocysts, each sporocyst contains 2 sporozoites. For the Cryptosporidium oocyst there are no sporocysts, in a sporulated oocyst we see directly 4 sporozoites.
The main difference between the oocysts of Cryptosporidium and Cyclospora cayetanensis is their size. Cryptosporidium oocysts are smaller, measuring 4-6 micrometers in diameter, while Cyclospora oocysts are larger, measuring 7-10 micrometers in diameter. This difference in size is important for diagnostic purposes and helps in differentiating between the two parasites.
I agree with Azza and Aissa: the non-overlapping size is probably the most crucial characteristic for differentiating both of these parasites.
I would like to add also that Cyclospora oocysts will demonstrate auto-fluorescence, while Cryptosporidium oocysts will not. Finally, both parasites are often foodborn, but Cryptosporidium can also be waterborn or zoonotic.
The oocyst size (referred to in the earlier postings here) made me realize that what is now known as Cyclospora is similar to a coccidian parasite that had been found in Papua New Guinea, as reported in an article with which I was familiar (see the first reference in the first publication listed below). This occurred to me before the nature of Cyclospora had been identified by others as coccidian; but at the time, I did not publish my thoughts on the matter.
Various coccidia have been found to be detectable by acid-fast oocyst staining (see the other two publications listed below).
REFERENCES:
Markus MB, Frean JA. 1993. Occurrence of human Cyclospora infection in sub-Saharan Africa. South African Medical Journal 83 (11): 862–863. http://archive.samj.org.za/1993%20VOL%2083%20Jan-Dec/Articles/11%20NOVEMBER/1.13%20LETTERS.pdf
Bush JB, Markus MB. 1987. Staining of Isospora belli oocysts. Transactions of the Royal Society of Tropical Medicine and Hygiene 81 (2): 244.
Markus MB, Bush JB. 1987. Staining of coccidial oocysts. Veterinary Record 121 (14): 329.
The main difference between the oocysts of Cyclospora and Cryptosporidium is their appearance and how they’re shed. Cyclospora oocysts are larger and round, often glowing under UV light, while Cryptosporidium oocysts are smaller and more oval-shaped. Cyclospora’s oocysts need to mature outside the body to be infectious, whereas Cryptosporidium’s oocysts are infectious right after they’re passed.