Microarray-based genomic technology provides a promising high-throughput alternative to traditional methods in detection and identification of microorganisms in environments. The objectives of this project were 1) to investigate the airborne fungi community structures along urban-rural gradients and their seasonal fluctuations; 2) to monitor airborne fungal flora of fungal allergic patients’ home when they with/without symptoms of allergy by viable count, direct count and microarray; 3) the results provided references for environmental policy. Both indoor total culturable fungi concentrations and their I/O ratios at patients' home had no correlation with allergy of 8 patients. The I/O ratios greater than one means there are fungal spores produced indoor, and the patients should be reminded to reduce allergens at home. Cladosporium oxysporum, C. cladosporioides, Aspgillus niger, A. flavus, Asp. Fumigates, Penicillium oxalicum, P. brevicompactum were major causes of sensitization in Taichung. With regard to fungus genus, Cladosporium was the most prevalent isolated genus and the allergenic threshold was > 50 CFU/m3. When patients showed allergic sensitization, in their home, concentrations of Aspergillus / Penicillium species were from 10 to 35 CFU/m3. The allergic threshold level of Aspergillus and Penicillium was > 10 CFU/m3. The airborne fungal flora had seasonal variations in Taichung and no significant difference between urban and suburban. The spore concentrations of the samples collected from the home of participants and Taichung city were estimated by interpolation based on the Microarray signal data were corresponded with spore concentrations of those samples counted by viable counts. The detection and identification of microorganisms by this Microarray kit was feasible. The bottleneck of the application of Microarray kit was discussed.