Bacterial and fungal contamination in the air and settled dust were studied in old and new book libraries located in the National Research Center (NRC), Dokki, Giza, Egypt. The investigated libraries differ in age, design, size, ventilation type, and number of occupants in relation to microclimatic parameters and particulate matter (PM) load. Airborne microorganisms were collected using an Andersen two stage impactor sampler. Indoor airborne bacteria and fungi ranged from 0-1060.4 CFU/m3 and 11.8-315.6 CFU/m3, respectively. Outdoor airborne bacteria and fungi ranged within 11.7-2514.7 CFU/m3 and 0-713.7 CFU/m3, respectively. Bacteria and fungi associated surface settled dust ranged from 0.4-10x106 CFU/gm and 0-73x104 CFU/gm, respectively. Fine microbial fraction (particles ≤ 8 μm in size) constituted 2-24.94% and 68.35-94.15% of the total airborne bacterial and fungal concentrations, respectively. Indoor/outdoor (I/O) ratios of airborne microorganisms were less than 1 at both libraries, indicating no indoor microbial sources. Gram positive cocci (14.3-47%) and bacilli (52.9-85.7%) were the dominant bacterial isolates in the air state, while bacilli represented 100% of the total isolates in the surface settled dust. Bacillus pseudomycoides and B. subtilis dominated indoors while B. subtilis and Staphylococcus outdoors. Aspergillus and Penicillium, were the common fungal species in both libraries under investigation. Many of the isolated fungal taxa had enzymatic activities (lipase, protease and cellulase), with A. flavus, Curvularia pallescens, Fusarium oxysporium, P. notatum and Trichoderma viride presented all enzymatic activities. Complex correlations and no-clear patterns were found between the airborne microorganisms and the environmental factors.