Abstract: In various aspects, a multiplex primer set, a kit for performing an assay to detect microsporidia, and a method of identifying a microsporidia in a sample is provided. The multiplex PCR primer set including SEQ ID NOS 1-4. The kit includes a multiplex PCR primer set having SEQ ID NOS 1-4 and a set of probes having SEQ ID NOS 5-8. In the method a sample is obtained and a multiplex PCR assay is performed on the sample. A multiplex PCR primer set including SEQ ID NOS 1-4 is included in the multiplex PCR assay. The sample is determined to have the microsporidia in response to the multiplex PCR assay amplifying a target sequence associated with microsporidia.