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Background  Molecular research revealed that some of the European  Calypogeia  species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification.    Results  On the basis of 22 individuals, representing 10  Calypogeia  species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in  C. suecica , as our results indicate. Having the sequences of entire plastomes of European  Calypogeia  species, we also discovered that the  ndhB  and  ndhH  genes and the  trnT-trnL  spacer identify species in 100%.    Conclusions  This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called “specific barcodes” for a given taxonomic group, based on plastome data.

Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes