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Multilocus phylogenetic analysis of small-subunit (SSU) rRNA and actin from Cryptosporidium molnari clustered this species with the C. molnari-like genotype of an isolate from the guppy, although the two fish isolates seem to be distinct species. The analysis of available piscine genotypes provides some support for cladistic congruence of the genus Piscicryptosporidium, but additional piscine genotypes are needed.

Molecular Characterization of Cryptosporidium molnari Reveals a Distinct Piscine Clade