Giardia duodenalis is one of the most prevalent intestinal protozoa infecting humans and domestic animals. The aim of this study was to identify subspecies of G. duodenalis by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method from fecal samples of naturally infected cattle in the Urmia, West Azerbaijan province, Iran. Overall, 246 fecal specimens were collected from the cattle (diarrheic and healthy) and microscopically examined for G. duodenalis. The PCR-RFLP analysis of glutamate dehydrogenase (gdh) locus was used to identify the genotypes found in cattle. In this method, 432 bp expected size was amplified and then specific restriction NlaIV enzyme was used for subspecies detection. Totally, 23 (9.34%) specimens were microscopically positive for giardiacyst out of 246 examined samples. The PCR-RFLP analysis revealed that 19 samples (82.60%) have the genotype E and 4 samples (17.39%) belong to the subgroup AI. Our findings indicated that G. duodenalis infection is prevalent in cattle of Urmia and the non-zoonotic genotype E predominates in cattle in this region.