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The aim of the study was to detect the infection level of honey bees with Nosema apis and/or Nosema ceranae using microscopic and molecular analysis from indigenous honeybee race of eight Saudi Arabian geographical regions. A detailed survey was conducted and fifty apiaries were chosen at random from these locations. Infection level was determined both by microscope and Multiplex-PCR and data were analyzed using bioinformatics tools and phylogenetic analysis. Result showed that N. ceranae was the only species infecting indigenous honeybee colonies in Saudi Arabia. As determined by microscope, Nosema spores were found to be in 20.59% of total samples colonies, while 58% of the samples evaluated by PCR were found to be positive for N. ceranae, with the highest prevalence in Al-Bahah, a tropical wet and dry climatic region, whereas low prevalence was found in the regions with hot arid climate. Honeybees from all eight locations surveyed were positive for N. ceranae. This is the first report about the N. ceranae detection, contamination level and distribution pattern in Saudi Arabia. (C) 2017 The Authors. Production and hosting by Elsevier B.V. on behalf of King Saud University.