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Molecular tools have been developed to detect and differentiate Cryptosporidium at the species/genotype and subtype levels. These tools have been increasingly used in the characterization of the transmission of Cryptosporidium spp. This review addresses the most recent developments in molecular epidemiology of cryptosporidiosis.The recent development of subtyping tools has led to better understanding of the population genetics and transmission of Cryptosporidium in humans. The population structure of C. parvum and C. hominis is apparently more complicated than previously suggested, with the likely existence of both clonal and panmictic populations. Thus, the transmission of C. parvum (genotype II) in humans is shown to be different in different areas, with zoonotic transmission important in certain places and anthroponotic transmission in others. The use of molecular tools has also led to the identification of geographic and temporal differences in the transmission of C. parvum and C. hominis, and better appreciation of the public health importance of other Cryptosporidium species/genotypes and the frequency of infections with mixed genotypes or subtypes.Factors involved in the transmission of human cryptosporidiosis are difficult to examine using conventional methods. The use of molecular tools has been helpful in the assessment of the zoonotic potential of various Cryptosporidium spp. and sources of human infections, and has started to play a significant role in the characterization of transmission dynamic in endemic and epidemic areas.