Domestic animals play a vital role in the spread and transmission of various zoonotic agents to humans. Giardia duodenalis, an important enteric zoonotic parasite, is widespread globally. This research aimed to assess the presence and genetic diversity of G. duodenalis assemblages in domestic animals in Shiraz, southern Iran. 245 fresh fecal samples were collected from 87 dogs, 63 cats, and 95 cattle in Shiraz, the capital city of Fars province, between July 2021 and August 2022. None of the animals showed gastrointestinal signs such as diarrhea, and all fecal samples had normal consistency. Upon parasite observation using light microscopy, a DNA fragment of G. duodenalis tpi gene was amplified using nested-PCR. Using direct wet mount and Wheatley’s trichrome staining examination, 9 out of 245 samples (3.7%; 1 from dogs and 8 from cattle) tested positive for G. duodenalis. Molecular methods confirmed 1.1% (1/87) of dogs and 8.4% (8/95) of cattle to be positive. Giardiasis was not detected in cats. Phylogenetic analysis revealed that Giardia isolates infecting dogs and cattle in Shiraz belonged to three genotypes/assemblages: A, B (zoonotic), and E (non-zoonotic). In cattle, assemblages E (75%; 6/8), A (12.5%; 1/8), and B (12.5%; 1/8) were identified, while dogs were infected with assemblage A (100%; 1/1). In Shiraz, southwestern Iran, domestic animals like cattle and dogs could potentially serve as reservoirs for zoonotic infections caused by G. duodenalis.