Schistosoma japonicum obtained from Taiwan is a zoophilic strain that only infects domestic and small animals. Recombinant fructose-1,6-bisphosphate aldolase (FBPA) derived from this strain was used as an antigen in an enzyme-linked immunosorbent assay (ELISA) for the diagnosis of human schistosomiasis. The full-length DNA sequence of FBPA was found to be 1092 bp, encoding a protein of 363 amino acid residues, with a molecular mass of 39.6 kDa. A total of 120 participants were recruited from China and Taiwan to evaluate the diagnostic value of this recombinant protein. In these participants, 34 were found to be infected with S. japonicum, 16 with Ascaris lumbricoides, 15 with hookworm, 13 with Paragonimus westermani and 13 with Clonorchis sinensis, whereas 29 had no ova on faecal examination. Western blot analysis showed that the recombinant FBPA reacts strongly with schistosome ova-positive sera. The sensitivity and specificity of ELISA with FBPA were found to be 85.3% and 93.0%, respectively. These results indicate that FBPA derived from the Formosan strain of S. japonicum can be used for the diagnosis of human schistosomiasis.