Intestinal parasites, both helminths and protozoa, are commonly found in domestic animals, and the possible transmission of enteric parasites from dogs and cats to humans may constitute a global potential health risk worldwide. In the present study, we analysed 148 stool samples from dogs (n=126) and cats (n=22) collected from animal shelters and veterinary clinics, in the district of Évora, Portugal. Microscopic examination confirmed that Giardia was the most frequent parasite in the studied population (34/148; 23%). Other parasites such as Ancylostoma sp., Isospora spp., Toxocara, Trichuris spp., Toxascaris and Toxoplasma were also found. Furthermore, molecular characterization of Giardia duodenalis analysis targeting the small subunit ribosomal RNA (ssu-rRNA) was performed revealing the presence of host-specific (C and D) and zoonotic assemblages (A and B). This work points out to the importance of protozoan parasites in companion animals, and reanalyses the need for parasite prophylaxis.