Cryptosporidium is an apicomplexan zoonotic parasite that infects most mammals, including humans. Cryptosporidium parvum virus type 1 (CSpV1) is the first member within the Partitiviridae family recognized to infect protozoan hosts. Cryptosporidium tracking based on CSpV1 detection has been attempted; however, each study used different conditions for the PCR protocol, primers, and target viral sequences. Accordingly, the sensitivity of PCR-based CSpV1 detection remains unclear. In addition, oocyst purification from clinical samples can be problematic due to small number of oocysts, sample degradation and low yield efficiency of currently used purification methods. Here we show that the second half of the coding region of dsRNA2 can be detected from various types of clinical samples, without the need for oocyst purification, by using a semi-nested-PCR technique. Furthermore, we show that the short sequence targeted in this study has higher diversity than the Cryptosporidium GP60 gene. Taken together, our findings suggest that this method could be used as an important tracking marker for Cryptosporidium species