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Background  Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European  Phoxinus phoxinus  species complex was used.    Results  The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely  P. ketmaieri ,  P. likai , and  P. apollonicus . For three species ( P. strandjae ,  P. strymonicus, P. morella ), further investigation with increased data sampling was suggested, while two primary hypotheses,  P. bigerri  and  P. colchicus , were supported as secondary species hypotheses. Finally, six of the primary species hypotheses ( P. phoxinus ,  P. lumaireul ,  P. karsticus ,  P. septimanae ,  P. marsilii  and  P. csikii ) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis.    Conclusion  The approach has proven useful for revision of species complexes, and the study can serve as an overview of the  Phoxinus  genus in Europe, as well as a solid basis for further work.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-017-1032-x) contains supplementary material, which is available to authorized users.

Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European Phoxinus (Cyprinidae)