At one time it was thought that Cyclospora was a blue-green alga because it appeared to share some structural and chemical features with this group of prokaryotes. Later observations revealed that Cyclospora is a eukaryotic organism related to the coccidian parasites Cryptosporidium and Isospora and more distantly related to the microsporidia Septata and Enterocytozoon . As recent outbreaks have demonstrated, however, immunocompetent individuals are also at risk for infection. When the merozoites are released from the enterocytes, they disperse to infect other intestinal cells. There may be one or many cycles of this type of asexual reproduction and then a cycle of sexual reproduction producing gametes.
Fertilization results in the formation of oocysts, which are then passed out with the feces.
In some protozoa, such as Cryptosporidium , the oocysts are immediately infective to another host while in others, e.g. Cyclospora and Isospora , the oocysts must mature for several days or longer before becoming infective. Infectious stages of Septata and Enterocytozoon are called spores. When these are ingested and reach the small intestine, the spore contents are injected directly into an enterocyte. These parasites then multiply within the host cells and carry on many cycles of asexual reproduction. It has been hypothesized that invasion of the intestinal cells stimulates the release of cytokines which activate phagocytes.