Nosemosis is one of the most prevalent bee diseases in the world causing significant economic losses in the global bee-keeping industry. This cross-sectional study was conducted during April-September, 2016 to investigate the prevalence of nosemosis in different climatic regions of Iran. A total of 183 apiaries were selected based on cluster sampling and the climate of apiaries under study was classified using Domarten method. In each apiary, five percent of the colonies were randomly sampled. A total of 183 adult bee samples were taken and examined by microscopic and polymerase chain reaction (PCR) methods for the presence of Nosema infections. According to the results, infection caused by Nosema ceranae was observed in all regions under study. The prevalence of N. ceranae was 46.40% (42.70–50.10). However, infection with Nosema apis was not observed in the samples in either pure form or as associated infection. Based on the results of PCR, the prevalenceof N. ceranae was 53.80% (46.60– 61.00) in humid, 71.00% (53.70–77.50) in semi-humid, 68.10% (61.40–74.80) in very humid, 29.40% (22.70–36.10) in arid, 34.30% (27.40–41.20) in semi-arid and 24.00% (17.90–30.00) in Mediterranean climates. The prevalence of infection in different climatic zones of the country was found to have significant differences (p < 0.001). According to the findings, N. ceranae was the only Nosema species in honeybees with a broad geographical dispersion in Iran. It seems that climate can influence the prevalence of mentioned parasite.