The nucleotide sequence of the second internal transcribed spacer (ITS-2) from ribosomal DNA has been determined for 3 members of the Hypodontus macropi species complex. Sequences were compared from nematodes collected from 3 species of Australian macropodid marsupial, Petrogale persephone, Macropus robustus robustus and Thylogale billardierii. The ITS-2 of each operational taxonomic unit ranged from 287 to 292 bases in length, and had a GC content of 36.6-40.1%. Differences in nucleotide sequence between nematodes from the different host species ranged from 25.0% to 28.3%. The data suggest that H. macropi from P. persephone represents a different species to those in M. r. robustus and T. billardierii. The unique feature of this study is that it represents a comparison of the ribosomal DNA sequences of nematode species which are morphologically indistinguishable but which have been demonstrated to be genetically distinct (i.e. cryptic) species based on electrophoretic data. The results also demonstrate further that morphological characters alone are often not adequate for species recognition. Differences between these 3 species of H. macropi in their recognition sites for restriction endonucleases, indicates that a PCR-RFLP approach could be used, in conjunction with allozyme electrophoresis, to establish how many species are present within the H. macropi complex.