The identification of Cryptosporidium oocysts in environmental samples is largelymade by the use of immunofluorescent assay (IFA). Because IFA detects oocystsfrom all Cryptosporidium parasites, the species distribution and source ofCryptosporidium parasites in environmental samples is unclear. The authorspreviously developed a small subunit (SSU) rRNA-based polymerase chainreaction-restriction enzyme length polymorphism (PCR-RFLP) technique for species-and strain-specific diagnosis of Cryptosporidium parasites in clinical samples.In this study, the authors used this technique in conjunction with immunomagneticseparation to identify species and sources of Cryptosporidium oocysts present inwater samples. Twenty-nine storm samples collected after 8 rain events weretested with this technique. Includes 30 references, table, figures.