Giardia duodenalis is a cosmopolitan intestinal protozoan that affects a wide range of vertebrates, including humans, and domestic and wildlife animals. Genetic characterisation identified 8 different genotypes within the G. duodenalis species complex, known as Assemblages A to H. Assemblages A and B have been reported mainly in humans. Molecular characterization studies of Giardia isolates from cats have reported mainly the presence of Assemblage F, but Assemblage A has also been reported, implying a potential transmission of G. duodenalis from cats to humans. Little is known about the prevalence and Giardia genotypes that infect cats, in Portugal. In addition, several fenbendazole treatment-refractory cases of cat giardiasis have been reported by clinicians. As such, this study aimed to determine the prevalence of Giardia spp. and other enteric pathogens, their distribution into assemblages, and the sympatric circulation of assemblages associated with the refractory treatment of cats from Portugal.