Polymerase chain reaction specific for the rDNA marker for Nosema ceranae and Nosema apis was conducted on 84 Apis mellifera samples collected from 20 provinces in Turkey. N. ceranae was detected from three samples from the provinces of Artvin, Hatay, and Mugla. N. apis was detected in samples from the provinces of Sivas, Izmir, Bitlis and Gaziantep. All of the positive samples were from honey bees belonging to the 'C' lineage of A. mellifera. DNA sequencing analysis of the N. ceranae samples revealed that there was no intraspecific variation in the 208 bp of the 16S SSU of N. ceranae from Turkey. A TCS analysis revealed that the 16S SSU genotype from Turkey is identical to N. ceranae DNA sequences from Europe, Australia, and the United States. TCS analysis also revealed that this genotype is the basal ancestral genotype among six N. ceranae genotypes. This is the first study to confirm that N. ceranae is present in honey bees from Turkey.