Many airborne fungi associated with respiratory allergy. An accurate, fast and high throughput technique is demanded to detect and monitor allergenic fungi in the air for environment protection, public health and clinics needs. In this study, we develop a microarray detection technique for airborne allergic fungi by quantitative Nuclease Protection Assay System and large-volume air samples collection method. This microarray contains 16 specific probes for 14 target fungal genera/species, including 9 species-specific and 7 genus-specific probes. Decent calibration curves were generated and R-squares＞0.9. The detection limit was 15 - 90 spores/m3 air. Ninety-six samples are able to be processed by the microarray technology simultaneously, which reduce bias among batches and decrease time and labor consuming for practical application of large number samples’ routine detection. To study the airborne allergic fungi in Taiwan, we investigated the fluctuation of airborne fungal spore at patients’ home when patient with / without syndromes. The protocol could be used to establish the airborne allergic fungal list in Taiwan.

allergy, fungal spore, airborne, microarray, probe, detection