Abstract: The purpose of this study was to investigate the genotypes of Giardia duodenalis from human and animal feces and their epidemiological in Iran. Molecular characterization of cysts of human and animal origin represents an objective means to approve or reject this hypothesis. In this study, cysts of Giardia duodenalis were collected from feces of naturally infected cats (n = 2), human (n = 34), dog (n = 2) and cattle (n = 3). PCR-RFLP analysis of the 34 specimens recovered from humans revealed 6 G. duodenalis assemblage AII, 8 G. duodenalis assemblage BIII and 4 G. duodenalis assemblage BIV. Among samples from cats, 1 was classified into assemblage AI. Genetic subgenotypes identified from human reveals that genetic diversity of this protozoan in East Azerbaijan, Iran, is similar to that of Giardia from other parts of the world. The present study represents the first contribution to the knowledge of G. duodenalis genotypes in Iran.