Giardia duodenalis is a protozoan parasite found in humans and many mammals. This parasite spreads worldwide and is generally recognized as a zoonotic agent and is reported to be one of the most common causes of diarrhea in humans and animals. In this study, it was aimed to determine the prevalence and genotypes of Giardia duodenalis in shelter dogs in Diyarbakır province located in the Southeastern Anatolia region of Turkey. Native-Lugol method and nested PCR analyses of 100 fecal samples showed a prevalence of 3% and 4%, respectively. The prevalence was higher in females and in those younger than one year. Sequence analysis revealed the presence of zoonotic Assemblage B, Assemblage D, and Assemblage E. The detection of zoonotic Assemblage B in this study suggests that dogs may be a reservoir for human giardiasis. Further molecular research is needed to determine the genotype diversity of Giardia as well as its possible role in the transmission of this parasite to humans.