Cryptosporidiosis is one of the most important parasitic infection in sheep. The aim of the present study, was to identify species of Cryptosporidium isolated from sheep in Tehran province based on HSP70 gene by Nested PCR-RFLP assay. In the first step 1485 faecal samples were collected form sheep in Tehran province then the samples were examined for Cryptosporidium detection using modified acid fast staining. In the second step DNA of the positive samples were extracted, then gene ofHSP70 was amplified by Nested-PCR in order to differentiate between species. The PCR product was digested by Hind II restriction enzyme. According to the result, 22 positive sheep samples were detected by modified acid fast method. The results were confirmed by molecular technique. The 800 bp fragment of HSP70 digested by restriction enzymes. Twenty samples showed similar band on 2.5% agarose gel whereas 2 samples demonstrated different pattern. Based on sequence results, the first and second groups were identified as Cryptosporidium andersoniand C.parvum respectively. Generally, in spite of Cryptosporidium parvum introduced as the major agent of cryptosporidiosis in sheep but in our study Cryptosporidium andersoni was dominant.