Recent foodborne disease outbreaks caused by Cyclospora cayetanensis has increased the interest in the development and application of methods to detect this organism in foods. A PCR test to detect Cyclospora by amplifying a region of the Cyclospora 18S ribosomal RNA gene has been developed (Relman et al. 1996; Yoder et al., 1996). However, the test also yields an amplicon of the same molecular size when DNA from the closely related genus of coccidian parasite, Eimeria, is available as a template. Eimeria spp. may infect a wide range of non-human hosts. Therefore, it is important for this method to distinguish between these genera for the application of this PCR based test to food and environmental samples. Although the 18S rRNA gene nucleotide sequences of Cyclospora and Eimeria spp. are 94-96 percent similar, there are specific nucleotide differences in the amplified segment. An RFLP analysis was developed using the Mnl I restriction enzyme to differentiate between the PCR amplicons produced by these two genera.