Giardia-like microorganisms were found as a result of a Cryptosporidium/Giardia detection assay on winter reservoir samples. The morphological aspects, DNA sequence of the microorganism, and specificity of immunoassay reagents were investigated. The microorganism was very similar to a Giardia cyst. The cell was oval shaped (11.0 μm in length, 7.7 μm in width), contained organelles and was stained bright apple-green by a fluorescent monoclonal antibody, although no axonemes or curved bristles were observed. Cross-reaction occurred with the anti-Cryptosporidium, but not the anti-Giardia, immunomagnetic antibody. The specificity of the fluorescent monoclonal antibodies differed depending on the product. As a result of the analysis of the partial sequence of 18S rDNA, the microorganism was identified as Lunulospora curvula, mitosporic Ascomycota. These findings will be very helpful for avoiding false positives in future assays.