Cortinarius koldingensis is described as a new species based on several collections from a small area in Denmark. Sequence data from the ITS marker places it in the Sulfurini group of the large Calochroi clade of Cortinarius subgenus Phlegmacium, along with C. sulfurinus and two North American taxa. It is phylogenetically distinct from the other species in the Sulfurini and differs from C. sulfurinus by several deviating morphological characteristics. The species has been collected on several occasions over the last 15 years from only one Danish locality. Despite extensive molecular screening of numerous possible conspecific specimens, including holotype and comparison with all publicly available ITS sequence data from specimens and environmental DNA alike, no match with specimens from elsewhere has been encountered, and we hypothesize that the species is rare in Europe.