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.