Cryptosporidium parasite is a cause of diarrhea in humans and other cold and endotherm animals that have been widely distributed throughout the world. This study aimed to determine the genetic diversity of Cryptosporidium in children with diarrhea using the GP60 gene by Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) method. In this study, stool specimens were collected from 182 children with diarrhea referring to Zabol hospitals. By direct observing the direct wet smear, Sheather's Sugar Flotation Solution, and Ziehl-Neelsen staining, examinations were conducted to identify the parasite, eventually, on DNA Extracted from isolates, PCR-RFLP was performed. From the total of samples of 182 stool specimens, 27 isolates were diagnosed infected with Cryptosporidium using the Ziehl-Neelsen staining method, of which 17 isolates were from Cryptosporidium parvum and 10 isolates from Cryptosporidium hominis using molecular examinations. Both human and cattle genotypes of Cryptosporidium can be seen in children with diarrhea. However, given that the dominant species are Cryptosporidium parvum, the zoonotic transmission is more common than human transmission, and contact with livestock is considered as the most important source of human contamination.