The honeybee pathogens Nosema ceranae and deformed wing virus (DWV) cause the collapse of honeybee colonies. Therefore, it is plausible that these two pathogens act synergistically to increase colony losses, since N. ceranae causes damage to the mid-gut epithelial ventricular cells and actively suppresses the honeybees' immune response, either of which could increase the virulence of viral pathogens within the bee. To test this hypothesis we exploited 322 Hawaiian honeybee colonies for which DWV prevalence and load is known. We determined via PCR that N. ceranae was present in 89–95% of these colonies, with no Nosema apis being detected. We found no significant difference in spore counts in colonies infected with DWV and those in which DWV was not detected, either on any of the four islands or across the entire honeybee population. Furthermore, no significant correlation between DWV loads (ΔCT levels) and N. ceranae spore counts was found, so these two pathogens are not acting synergistically. Although the Hawaiian honeybees have the highest known prevalence of N. ceranae in the world, with average number of spores been 2.7 million per bee, no acute Nosema related problems i.e. large-scale colony deaths, have been reported by Hawaiian beekeepers.