Nosema ceranae has been suggested to be replacing Nosema apis in some populations of Apis mellifera honeybees. However, this replacement from one to the other is not supported when studying the distribution and prevalence of both microsporidia in professional apiaries in Spanish territories (transverse study), their seasonal pattern in experimental hives with co-infection or their prevalence at individual level (either in worker bees or drones). Nevertheless, N. ceranae has shown to present a higher prevalence at all the studied levels that could indicate any advantage for its development over N. apis or that it is more adapted to Spanish conditions. Also, both microsporidia show a different pattern of preference for its development according to the prevalence in the different Spanish bioclimatic belts studied. Finally, the fact that all analyses were carried out using an Internal PCR Control (IPC) newly developed guarantees the confidence of the data extracted from the PCR analyses. This IPC provides a useful tool for laboratory detection of honeybee pathogens.