The objective of this study was to compare the effectiveness of the multiplex PCR method and traditional light microscopy in identifying and discriminating the species of Nosema spp. spores in worker bees from winter hive debris in the Province of Warmia and Mazury (NE Poland). A total of 1000 beesdead after from the bottom of the hive from bee colonies were analyzed. Spores were identified with the use of a light microscope (400-600x magnification). Spores were assigned to species by the multiplex PCR method. The microscopic evaluation revealed the presence of Nosema spp. spores in 803 samples (80.3%). Nosema ceranae spores were observed in 353 positive samples (43.96%), Nosema apis spores were found in 300 samples (37.35%), while 150 samples (19.67%) showed signs of a mixed infection. A multiplex PCR analysis revealed that 806 samples were infested with Nosema spp., of which 206 were affected only by Nosema ceranae, 600 showed signs of mixed invasion, while no samples were infected solely by Nosema apis parasites. In two cases, the presence of spores detected under a light microscope was not confirmed by the PCR analysis. The results of the study indicate that Nosema ceranae is the predominant parasitic species found in post-winter worker bees from the bottom of the hive in the region of Warmia and Mazury.