Ligula (Cestoda: Pseudophyllidea) infections in gudgeon (Gobio gobio) and roach (Rutilus rutilus) differ markedly in the pathology that is observed in the host, particularly with respect to a tissue response and the extent of inhibition of gonadal development. The entire internal transcribed spacer (ITS) region (ITS-1, 5.8S and ITS-2) and the large subunit domains D1–D3 were sequenced and compared in parasites from these fish from Lough Neagh, Northern Ireland, together with a single specimen from minnow (Phoxinus phoxinus) from Wales. Sufficient differences were observed between parasites from R. rutilus and G. gobio to support the suggestion that they may represent different strains/species. In contrast, Ligula from P. phoxinus closely resembled those from R. rutilus. Ligula infections in G. gobio were recorded prior to the introduction of R. rutilus. The co-existence of separate strains or species of Ligula in Lough Neagh probably resulted from the introduction of R. rutilus to these waters, correlated with an increase in the number of great crested grebes (Podiceps cristatus).