Schistosomiasis is a parasitic disease transmitted through water by blood-fluke trematodes of the genus Schistosoma. After malaria and soil-transmitted helminthiasis, it is the third most important parasitic tropical disease. An estimated 236 million people are infected, with another 700 million at risk of infection. It is estimated that 90% of all schistosomiasis cases occur in Africa. The disease is regarded as a public health threat, with numerous debilitating effects on growth, well-being, and overall health. The importance of snail-intermediate hosts in schistosomiasis transmission cannot be overstated, and thus monitoring the prevalence and distribution of Schistosoma cercariae is critical for indirect estimation of schistosomiasis in human or animal populations. As a result, developing sensitive tools to aid in the characterization of specific schistosomes is critical, and this protocol outlines procedures ranging from DNA isolation to PCR and the expected outcomes from newly developed oligonucleotides.