The ribosomal RNA (rRNA) gene units of Schistosoma mansoni and S. rodhaini, of the lateral spined egg group, have been studied. The schistosome rRNA gene unit consists of a regular interspersion of the two genes encoding the large and small rRNA units with two spacers. The large spacer is not transcribed while the small spacer is part of the transcription unit. Variation in the rRNA gene unit between the two species is demonstrated to take the form of loss or gain of restriction sites within the non-transcribed and transcribed spacers. This variation has been demonstrated to enable the differentiation of S. mansoni from S. rodhaini by Southern hybridization analysis. In addition, a DNA clone representing a female specific, tandemly repeated sequence, is demonstrated to enable differentiation of S. mansoni and S. rodhaini using dot blot hybridization analysis.