Cryptic species, belonging to the 37 collar-spine Echinostoma group, were distinguished using nuclear rDNA ITS (884 bases) and mtDNA CO1 (257 bases) and ND1 (530 bases) sequences. Sequences were obtained from five 37 collar-spine species, Echinostoma trivolvis, E. paraensei, E. caproni, E. revolutum and E. sp.I, a parthenogenetic isolate from Africa. Three geographic isolates of E. caproni were compared. Average sequence divergence among the 37 collar-spine species range from 2·2% in the rDNA ITS through 8% for the CO1 and 14% for the ND1. In addition, genes were sequenced from 2 non 37 collar-spine species, E. hortense and an undescribed Australian species, E. sp. (Aus). For each gene, distances of terminals from a predicted ancestral sequence were calculated. These indicated that ND1 is diverging significantly faster than the other 2 regions. In the CO1 gene most substitutions are synonymous and saturation has been reached for the majority of pairwise comparisons. The ND1 gene exhibits greater pairwise divergence but less evidence of saturation due to weaker conservation of first and second codon positions. The ITS has no amino acid coding constraints and displays no evidence of saturation. Although all 3 regions successfully distinguished the nominal species, ND1 appears to be the most informative region for investigating relationships within the 37 collar-spine group.