Nosema apis is a pathogen spesific for the European honeybee, Apis mellifera L., while Nosema ceranae is specific for the Asian honeybee, Apis cerana. Turkey provides different environmental and host conditions for both Nosema species. The aim of the study is to determine the dynamic of N. cerenae and N. apis seasonal infection. A number of samples were collected from different apiaries between 2009-2016 years. The samples were kept at -20 degrees C in the laboratory. Light microscopy was used for spore counting and molecular techniques were used to identify the Nosema species. The results showed that winter season had an impact on the type of Nosema as well as on infection rates. The number of N. ceranae spores decreases significantly at low temperatures (<= 5 degrees C). The winter period was found to be the main factor affecting nosema infection level and dominancy of Nosema ceranae. Furthermore, co-infection of both species is an indicator of the dynamics of N. apis and N. ceranae. This study suggests, that there is a dynamic prevalence among the Nosema species depending of the average winter temperature and not a replacement of N. apis by N. ceranae.