Technical Abstract: The prevalence of Nosema ceranae in managed honey bee colonies has increased dramatically in the past 10 – 20 years worldwide. A variety of genetic testing methods for species identification and prevalence are now available. However sample size and preservation method of samples prior to testing have not been thoroughly explored. Here, we test sample sizes ranging from 10 to 100 bees per colony and the suitability of ethanol, isopropanol, ice, and freezing as preservation methods prior to genetic testing. Larger sample sizes of 50 and 100 bees (3.77 x 106 ± 1.83 x 106 nosema/bee ; P = 0.0461 and 4.80 x 106 ± 1.60 x 106 nosema/bee; P = 0.0055, respectively) had higher levels of nosema/bee than those pooled in groups of 10 (1.13 x 105 ± 6.01 x 104 nosema/bee). Freezing/cold storage without the addition of chemical preservatives also improved the reliability and suitability of samples Both POST and FRZR samples had higher levels of N. ceranae than either of the alcohol treatments (ETOH: P = 0.0016 and P = 0.0142, respectively or ISOP: P = 0.0019 and P = 0.0166, respectively) for genetic testing. Larger sample sizes and freezing/cold storage are recommending for diagnostic testing purposes.