Rodentolepis nana (syn. Hymenolepis nana) is a cyclophyllidean zoonotic enteric parasite with worldwide distribution. In humans, it is more prevalent in children, especially in temperate zones. A morphologically similar species of R. nana occurs in different rodents, including gerbils. In the present study molecular characterization of five isolates of R. nana from Rhombomys opimus in the Golestan Province (n= 2) and Razavi Khorasan Province (n= 3), both in north-eastern Iran, were analysed. After DNA extraction, the internal transcribed spacer 2 (ITS2) region of the R. nana isolates was amplified and sequenced, and genetic variation was analysed. Accordingly, two isolates from the Razavi Khorasan Province showed ITS2 signatures that differed from the isolates from the Golestan Province. The third isolate from Razavi Khorasan did not reveal these specific signatures, but exhibited sparse nucleotide polymorphisms in the ITS2 sequence. The ITS gene is conserved, and variation in this fragment could be an interesting subject for further inspection of existing variation in the genome of R. nana, among different domestic and wildlife host species and from different areas.