A phylogeny based on three mitochondrial genes supports the division of Schistosoma intercalatum into two separate species.

Two recognized strains of Schistosoma intercalatum, one from the Democratic Republic of Congo (DRC), formerly Zaire, and the other from Cameroon, have been investigated using DNA sequences from 3 mitochondrial genes, cytochrome oxidase subunit 1 (cox1), NADH dehydrogenase subunit 6 (nad6) and the small ribosomal RNA gene (rrnS). In addition, partial DNA sequences from the nuclear large subunit ribosomal RNA gene (lsrDNA) were included within the study. Although partial lsrDNA alone reveals little taxonomic information, phylogenetic analysis of the mitochondrial data demonstrates a clear dichotomy between the 2 purported strains and it is proposed that they should be treated as distinct taxa. The 'original' S. intercalatum now falls relatively basal in the S. haematobium group, while the proposed new species is more derived and sister taxon to S. bovis and S. curassoni.