Intestinal cryptosporidiosis is a diarrheal disease caused by protists of genus Cryptosporidium that infect a wide variety of hosts, primarily vertebrates. Due to the close contact between humans and their companion animals, especially dogs and cats, there is concern about the potential for zoonotic transmission of this enteric protozoan parasite by infected animals. This study aimed to perform a microscopic and molecular diagnosis of Cryptosporidium spp. in fecal samples from domiciled dogs and cats. One hundred and nineteen fecal samples were processed using sugar centrifugal flotation followed by molecular detection of Cryptosporidium spp. DNA using nested PCR. Subtyping of isolates positive for C. parvum was performed by sequence analysis of the 60 kDa glycoprotein gene (GP60). Cryptosporidium oocysts were detected in 7.8% (5/64) and 5.4% (3/55) of the fecal samples from dogs and cats, respectively. Cryptosporidium canis (n = 3) and C. parvum (n = 2) were the main species found in dogs, whereas C. felis (n = 3) was prevalent in cats. Subtype IIaA17G2R2 (potentially zoonotic) was identified in samples positive for C. parvum. Despite the low prevalence of Cryptosporidium observed in the domiciled dogs and cats, the presence of potentially zoonotic C. parvum in dogs evidences a public health concern. Further research is needed to better understand the epidemiology, source, and potential impacts of Cryptosporidium infection in cats and dogs.