62 samples containing oocysts of the C. parvum human genotype parasites were obtained from infected individuals from different geographic regions. Using published primers, a multilocus polymerase chain reaction was carried out to amplify the C. parvum human genotype TRAP-C2, Poly-T, SSU rRNA, 70 kDa heat shock protein (HSP70) and GP60 genes, and one microsatellite sequence (SSR-1). The extent of genetic variation within the human C. parvum isolates was assessed by multiple alignments of obtained nucleotide sequences followed by phylogenetic analyses. Results showed that multiple subgenotypes within the 62 isolates were observed at all six loci evaluated, including the microsatellite loci. The absence of recombination and the linkage disequilibrium in subgenotypes among the different genes examined supports a clonal population structure for C. parvum. The nucleotide sequences of the HSP70 and GP60 gene of various C. parvum human genotype isolates have been deposited in the GenBank database under the accession numbers AF401503 to AF401507, AF402289 to AF402293, and AF403161 to AF403164.