We have developed the HRM real-time PCR for differential detection of S. japonicum and S. mekongi in fecal samples of final hosts and in tissues of snail intermediate hosts. A single Schistosoma egg in a 100 mg fecal sample (equivalent to 10 EPG) or a single cercaria in tissues from 10 pooled snails can be detected. These detection are quite similar with single-species detection limits for S. japonicum [19] or S. mekongi [20] using a real-time PCR assay with fluorescence resonance energy transfer (FRET) hybridization probes. Similar levels of sensitivity have been found using SYBR green based real-time PCR; 10 EPG of S. japonicum in fecal samples could be reliably detected [15]. However, Zhou et al. [29] showed that the TaqMan real-time PCR assay can detect 1 S. japonicum egg in 500 mg fecal sample (equivalent to 2 EPG) [29].