Cryptosporidium is a parasitic protozoon with a wide range of vertebrate hosts. Cryptosporidiosis has been reported from numerous countries, including Iran. Molecular identification can be applied to characterize Cryptosporidium, of which there are over 30 species and 50 genotypes. Herein, we report the genetic diversity of Cryptosporidium spp. in Iranian dogs for the first time based on 18S ribosomal RNA gene sequencing. One hundred forty fecal samples of herd dogs were collected from Isfahan, central Iran. The samples were concentrated using sucrose flotation and subjected to Kinyoun staining. DNA extraction of positive samples was performed, and molecular diagnosis was carried out using highly specific seminested PCR for the characterization of Cryptosporidium species. Finally, sequencing and DNA analysis were performed to identify Cryptosporidium species. A total of 2.14% of herd dogs were positive for cryptosporidiosis in both microscopy and molecular methods. In all cases, the causative agent was identified as Cryptosporidium parvum. Dogs associated with positive samples had been in close relationship with livestock. Cryptosporidiosis in the herd dogs in Isfahan could be due to their close contact with animals, particularly cattle and sheep. Given that dogs with cryptosporidiosis lack clinical symptoms, they are a potential source of zoonotic transmission of this disease as they are companion animals for humans. Dogs with cryptosporidiosis are a potential source of the zoonotic transmission of this disease.