||The biological characteristics of ambient aerosols are poorly understood. Bioaerosols containing bacteria and fungal spore can be a health hazard. In fact, endotoxin of gram-negative bacteria and most of fungal spores have been recognized as common allergens that are associated with various allergenic responses and respiratory symptoms. Conventional sampling of bioaerosols using culture-based methods suffers from underestimation and poor reproducibility of measurements, because they depend on the culturability of microorganisms. Although alkanoic acids (<C20) have been proposed as indicators for assessing microbial contributions in ambient aerosols, these fatty acids can originate from other anthropogenic sources and are not specific enough for determining the microbial compositions as well as their mass contributions. It is obvious that more specific methods are required for estimating mass contributions of particular microbial communities in ambient aerosols and for assessing the human health impacts due to inhalation of microorganisms in a quantitative manner. In this research, we applied a biomarker approach to quantify the concentrations of endotoxin/gram negative bacteria and fungi in the atmosphere. The 3-hydroxy fatty acids (3-OH FAs) and ergosterol were selected as specific biomarkers of endotoxin/gram-negative bacteria and fungal biomass, respectively. Gas chromatography-mass spectrometry (GC-MS) was utilized for quantification of these biomarkers in ambient aerosol samples (PM2.5 and PM2.5-10) collected by high volume samplers. This study has demonstrated the use of biomarker-to-microbial mass conversion factors for estimating the gram-negative bacterial and fungal mass contributions in ambient aerosols. Overall, the gram-negative bacterial and fungal dry mass concentrations are on the order of 10 - 102 ng/m3, making a small contribution in the total ambient aerosol mass. However, the endotoxin levels measured, ranging from 2.7 to 20.2 ng/m3 in PM10, are high enough to possibly pose a health hazard. Source apportionment analysis was conducted for determining the potential sources of endotoxin and ergosterol in the atmosphere. The results indicated that endotoxin and ergosterol generally have statistical relationships with Ca2+ and K+ so that these biomarkers may originate from crustal sources, distant biomass burning and kitchen emission. Furthermore, high concentrations of airborne endotoxin and ergosterol were recorded in the sampling periods with low relative humidity (<70%) and northerly prevailing wind, which are the climatic characteristics of autumn and winter of Hong Kong due to the influence of the Asian monsoon system. The preliminary analysis of the 72 hours backward air mass trajectories suggests that the long range transport of these biomarkers, especially for ergosterol, from the Asian continent to Hong Kong is possible.