Hymenolepis spp. infections are often asymptomatic, especially in light cases. Heavy infections can induce enteritis with nausea and vomiting, diarrhea, abdominal pain, and dizziness. Genetic therapy is the most future promising trend for treatment and prevention so, a genotype map of different parasite on microorganisms must be done. A simple and rapid polymerase chain reaction/restriction fragment length polymorphisms (PCR/RFLPs) assay, using the common restriction endonucleases HindIII, Bg1I, EcoRI, BanII, SacII and SstII, is described to illustrate the genetic structure of both Hymenolepis species. All restriction endonucleases have been used to differentiate between both species and based on ~2200 bp long sequence of the 18S ribosomal RNA gene. H. nana and H. diminuta were undifferentiated when their 18S rRNA genes digested with HindIII restriction endonuclease. The two Hymenolepis were welldifferentiated when their 18S ribosomal RNA genes were digested with Bg1I and EcoRI restriction endonucleases. It's clear observed that BanII, SacII and SstII restriction enzymes could be used as a genetic marker for H. nana when the enzymes uniquely fragmented the 18S rRNA gene without digesting the gene of H. diminuta.