Three isolates of the genus Cryptosporidium, namely, Guangdong isolate, Anhui isolate and Jiangsu isolate from Mainland China, were identified and characterized genetically utilizing nuclear DNA regions of the small subunit of ribosomal RNA (SSU rRNA) and heat shock protein 70 gene (HSP70) as genetic markers. These two regions were amplified by PCR from DNA extracted from oocysts and amplicons of approximately 290 bp and 450 bp were produced, respectively. The amplicons were purified, cloned and sequenced. Sequences of 446 bp and 290-292 bp were obtained for the SSU rRNA and HSP70 regions, respectively. The obtained SSU rRNA and HSP70 sequences representing the three Cryptosporidium isolates were compared with those retrieved from the DNA database. Genetic analyses using either DNA region revealed that members of Cryptosporidium formed two clusters, with C. parvum, C. wariri, C. felis and C. meleagridis clustered together, while C. andersoni, C. muris and C. serpentis belong to the other cluster. Based on SSU rRNA and HSP70 sequences, both Guangdong and Anhui isolates of Cryptosporidium were identified as C. muris of the calf genotype (i.e., C. andersoni), whereas the Jiangsu isolate was identified as C. parvum of the calf genotype. The findings of the present study should have important implications for the diagnosis and control of Cryptosporidium infections in both humans and animals in China.