There are many reasons why fungi found indoors, much like fungi at large, are not easy to characterize using molecular methods. There are no reference DNA sequences for the majority of the described fungal species, and the majority of extant fungal species are not described. These complications place high demands on the reference databases and tools used and call for solutions that are not normally found in the molecular ecology toolbox. This presentation will discuss database and analysis solutions to allow high-precision studies of indoor fungi in an accessible and reproducible way.