Black species of the Verrucariaceae are often colloquially called "Tar Lichens". Such species are found in various unrelated clades of the family, particularly in lineages with aquatic or semi-aquatic lifestyles. The number of cryptic and semi-cryptic species is known to be high in genera such as Hydropunctaria, but a revision of herbarium samples of black freshwater Verrucariaceae showed that Verrucaria species of other lineages are also often misidentified if only morphological characters are used for identification. Morphological revision of old specimens and DNA barcoding of recently collected material revealed, that Verrucaria pachyderma is among the most frequent "false positive" identifications in such collections in Europe. Some unusual morphological variants of Hydropunctaria scabra and Verrucaria funckii are the most frequently misidentified look-alikes which can be difficult to separate from V. pachyderma by morphology alone. As a consequence of the frequent misidentifications Verrucaria pachyderma has to be considered a much rarer and potentially threatened species than previously thought. Furthermore, instead of a single widespread taxon with rather wide ecological amplitude, new data indicate the presence of at least three subclades wihtin a monophyletic Verrucaria pachyderma s.lat., with different ecological requirements, but all of them morphologically indistinguishable. The results of this case study point to the wider question how freshwater Verrucariaceae can be included in ecological studies, assessments of conservation priorities for streams and rivers, and habitat monitoring programs. Pros and cons are discussed for alternative workflows which include the option to partially replace or complement species level identifications by functional groups approaches.