Fungi of the Stachybotrys genus have been isolated from water-damaged buildings and S. chartarum in particular has been associated with sick building syndrome (SBS). Current methods for detection and species identification methods are slow or limited by detecting one species at a time. To ameliorate this, we constructed a microarray platform that detects twelve different species of Stachybotrys in each sample and 16 samples on each glass slide. Hybridization probes were successfully designed for the internal transcribed sequence 1 (ITS1) region which can be PCR-amplified in many species at once using general primers. ITS1 is sequenced in a large number of fungi and new species can therefore easily be added to the microarray. The method was tested by analyzing commercial and environmental samples. In all cases, the correct species gave the highest signal intensity at an acceptable background level. This rapid and simple multiplex technique will be useful in gaining a better understanding of the role of fungi in the indoor environment.