Objective To molecularly identify Nosema species in provinces of Isfahan, Fars, Chaharmahal and Bakhtiari. Methods One hundred and eighty adult honey bees suspected with nosemosis from provinces of Fars (different counties), Isfahan, and Chaharmahal and Bakhtiari were tested. In order to determine the species of Nosema, previously developed PCR and primers based on 16S rRNA gene were used. PCR products were purified and sent to the Korean company of Macrogen for sequencing. Results Only Nosema ceranae was determined in all samples based on their molecular profile. Sequences of the 16S rRNA gene were sent to GenBank/NCBI (samples accession numbers KP318660–KP318663). Conclusions This species currently exists in European honeybee apiaries of Apis mellifera in the studied provinces.