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Cryptosporidium species differ in host range. Parasite–host coevolution, host adaptation, and geographic segregation have led to the formation of subtype families with unique phenotypic traits within the major human-pathogenic species C. parvum and C. hominis. Transmission intensity, genetic diversity, and occurrence of genetic recombination and selective pressure have further shaped their population genetic structures. Panmixia appears to be common within the zoonotic C. parvum, especially its hypertransmissible IIaA15G2R1 subtype. Genetic recombination in C. hominis, in contrast, is more restricted to virulent subtypes, especially IbA10G2. Nonhuman primates and equine animals are commonly infected with genetically divergent C. hominis populations. Systematic studies of these and other host-adapted Cryptosporidium spp. are likely leading to improved understanding of population structures underlying …