Sequence data of two coding and three non-coding loci were used to study the taxonomic identity within and relatedness among seven previously defined cryptic species (CSP) of Phialocephala fortinii and Acephala applanata using two approaches of species recognition. Identification of taxonomic groups corresponding to CSP was ambiguous in some cases when applying solely the genealogical concordance phylogenetic species recognition (GCPSR) concept. The definition of groups corresponding to CSP using GCPSR was complicated due to shared sequence haplotypes between CSP, unresolved CSP for several loci, and possible introgression. GCPSR in conjunction with a population genetic approach improved resolution significantly and the CSP status could be confirmed for all seven CSP of P. fortinii s.l. The most critical step in both analyses was the definition of groups. The combination of several classes of markers differing in resolution helped to define species boundaries.
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