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Background  Recent molecular studies have discovered substantial unrecognised diversity within the genus  Diplostomum  in fish populations in Europe and North America including three species complexes. However, data from the first intermediate host populations are virtually lacking. This study addresses the application of an integrative taxonomic approach to the cryptic species diversity of  Diplostomum  spp. in natural lymnaeid snail populations in Europe with a focus on the ‘ D. mergi ’ species complex.    Methods  Totals of 1,909  Radix auricularia , 349  Radix peregra , 668  Stagnicola palustris  and 245  Lymnaea stagnalis  were sampled at five reservoirs of the Ruhr river system in Germany and screened for infections with  Diplostomum  spp. Cercariae were examined and identified alive, fixed and under scanning electron microscopy. Sequences from the barcode region of the cytochrome  c  oxidase subunit 1 ( cox 1) mitochondrial gene and from the internal transcribed spacer cluster (ITS1-5.8S-ITS2) of the rRNA gene were amplified for 51 and 13 isolates, respectively.    Results  Detailed morphological and molecular analyses provided evidence for three named species ( Diplostomum spathaceum ,  D. pseudospathaceum  and  D. parviventosum ), and a further four species-level lineages (‘ D. mergi  Lineages 2–4’ and ‘ Diplostomum  sp. Clade Q’ in the lymnaeid snail populations from the Ruhr river basin. The paper provides the first descriptions of molecularly identified cercariae of  D. spathaceum  and of the cercariae of  D. parviventosum , three lineages of the ‘ D. mergi ’ species complex and of ‘ Diplostomum  sp. Clade Q’.    Conclusion  The integration of molecular and morphological evidence for  Diplostomum  spp. achieved in this study will serve as a baseline for species identification of these important parasites of snail and fish populations and thus advance further studies on the distribution of  Diplostomum  spp. in Europe.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-0904-4) contains supplementary material, which is available to authorized users.

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Integrative taxonomic approach to the cryptic diversity of Diplostomum spp. in lymnaeid snails from Europe with a focus on the ‘Diplostomum mergi’ species complex