BACKGROUND: Diagnosis of schistosomiasis remains elusive soon after infection. We evaluated several diagnostic methods in a cluster of travelers simultaneously exposed to freshwater in South Africa. METHODS: Eosinophil count, schistosome antibody tests, stool and urine microscopy, and serum Dra1 PCR assays were performed at week 4-5 (w4-5, early symptomatic phase), week 7-8 (w7-8, praziquantel treatment), and week 12-14 (w12-14, post-treatment). Sequencing was done on serum of 3 patients to identify the species. RESULTS: Of the 34 travelers (16 adults, 18 children), 32 developed symptoms 2 to 6 weeks after exposure. A raised eosinophil count (>750/µL) count was seen in 12/33 at w4-5, and in 22/34 at w7-8. Schistosoma antibodies were detected in 3/33 at w4-5, in 12/34 at w7-8 and w12-14. The Dra1 PCR was positive in 24/33 travelers at w4-5, in 31/34 at w7-8, in 25/34 at w12-14, and at least once in all. Ova were absent in all urine and fecal samples obtained. Sequencing identified S. mattheei nuclear and S. haematobium mitochondrial DNA, indicative of a hybrid species. CONCLUSION: The Dra-1 PCR confirmed diagnosis in all exposed travelers at a much earlier stage than conventional tests. The causative species is probably a S. mattheei x S. haematobium hybrid.