This paper discusses genetic markers capable of distinguishing between different sources of Cryptosporidium parvum to better understand the transmission and genetic heterogeneity of C. parvum. Using a combination of several restriction fragment length polymorphism (RFLP) markers, C. parvum isolates originating from different host species and different geographical origins were subjected to genetic fingerprinting using multiple RFLP markers. Since these markers were shown to reside on different chromosomes of C. parvum, this analysis allows not only the identification of different genotypes but could potentially reveal the presence of recombinants. In our sample of 28 isolates 41% were of genotype H, 52% of genotype C and 7% were mixed. Significantly, no H/C recombinants were detected, suggesting reproductive isolation between H and C parasites.