Airborne bacteria and fungi were analyzed during November, 2013. Morbidity due to respiratory diseases was alsoreported. The studied zones include Al-Mafraq downtown, Al al-Bayt University, Al-Zaatari refugee camp and the opendesert. A total of sixty air samples were collected by a microbiological air sampler on nutrient and tryptic soy agars ascultivation media for bacteria. Potato dextrose, Sabouraud dextrose and malt extract agars were used as cultivation mediafor fungi. Statistical analysis revealed that there was a significant difference between almost all studied zones (P<0.05).The highest bacterial level was detected in Al-Mafraq downtown with 2055 CFU m-3, whereas the lowest level wasdetected in the open desert with 23 CFU m-3. The highest level of fungi was detected in Al-Zaatari refugee camp (405CFUm-3), whereas the lowest level of fungi was observed in the open desert zone (13 CFUm-3). Bacteria and fungi levelswere within the suggested threshold value limits for culturable bacteria and fungi. Eleven different bacterial species andfour fungal species were isolated from these zones and identified by biochemical and molecular techniques. Fungi wereexamined macroscopically and microscopically and compared to the morphology of published fungal species. Theidentified bacterial species were Bacillus cereus, Bacillus aerius, Bacillus safensis, Bacillus subtilis, Bacillus axarquiensis,Bacillus pumilus, Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus methylotrophicus, Bhargavae acecembensis,and Cellulomonas sp. The isolated bacteria were all aerobic, Gram-positive, endospore-forming bacteria and catalasepositive. The identified fungi were Aspergillus niger, Aspergillus fumigatus, Penicillium sp. and Fusarium sp. In respect torespiratory diseases in the studied area, the most frequent lung diseases in the studied area was bronchitis (42%), followedby chest infection (25%), pneumonia (21%), and chronic obstructive pulmonary diseases (12%).In conclusion, the isolatedmicrobial species may appear to originate from the dusts of human and animal.