A new species of Chaenotheca, C. biesboschii, has been found in the freshwater tidal area of the Biesbosch in the Netherlands, a national park well known for harbouring several rare and threatened mosses and lichens. A phylogenetic analysis of the ITS region revealed some strongly supported infrageneric clades in Chaenotheca which were given informal names, and some were assigned provisional names in anticipation of generic recognition. The analysis also showed that the new species differed in the sequenced region from other European Chaenotheca species. Chaenotheca biesboschii might be mistaken for C. gracillima but, in addition to a considerable difference in the ITS region, it also differs from this species in morphology. It is also similar to C. servitii but again differs in morphology. Chaenotheca biesboschii inhabits decorticated wood in the oldest stages of forest development of abandoned willow coppices. In 2016 and 2017 a fairly large population was found in an area comprising several square kilometres. In the Biesbosch area, extensive woodlands have developed only since the 1950s and therefore C. biesboschii might have been recently established in the area, possibly following climatic warming. The new species is characterized by having an immersed, glaucous green thallus; apothecia 0·9–1·4 mm high; capitulum on the lower side when young with a ring-like thickening covered by a yellow pruina; when mature with a rusty brown pruina on the capitulum and upper part of stalk; spherical spores, 3·5–5·5 µm diam., ornamented by irregular cracks, medium brown; photobiont Stichococcus. A key to the European species of Chaenotheca is provided.