This study aims to investigate the airborne microorganisms and bacteria endotoxins in the poultry slaughterhouses, for understanding biological hazards in Taiwan poultry slaughterhouses. Three poultry slaughterhouses were selected as the testing subjects. The bacteria and fungi bioaerosol distributions were sampling by impactor bioaerosol sampler. The species of bioaerosol samples in the operating environment were finally purified, cultured, and further identificated of molecular biology. The results showed that in the poultry slaughterhouses, the highest average bacteria bioaerosol concentration was in the range of 1.67±0.15×10⁵ CFU/m³, and the highest average fungi bioaerosols concentration was about 8.35±0.32×10⁴ CFU/m³. According to the identificated of molecular biology in the poultry slaughterhouses, Staphylococcus spp., Moraxella spp., Bacillus spp., and Thermomonas spp. were the major bacteria; Pseudozyma spp., Penicillium spp., and Cladosporium spp. were the major fungi. The sampling data showed that the major bacteria bioaerosol distribution area were mooring area and slaughter area; fungi bioaerosol were distributing in slaughter area and cutting and packing area. Thus, the poultry slaughterhouses should increase the air exchange volume for decreasing bioaerosol concentrations. And according to the questionnaire analysis, the workers were negligent in personal protection.