Introduction Bioaerosols play an important role in incidence of infections in indoor and outdoor air of hospitals. Microorganismsplay a critical role in the health ofhuman beings and they are found everywhere in the environment, including different wards of a hospital. So, quantitative and qualitative analysis of microorganisms is highly important in hospital air. The aim of this study was to evaluate the diversity and density of bacteria and fungi in the air of Shohadaye Mehrab Hospital in Yazd City, Iran. Materials and methods Sampling was performed using a single-stage pump (Quick Take30) at a flow rate of 28.3 l per minute for five minutes. As a result, 288 indoor and outdoor hospital air samples were collected. Numbers and types of bacterial and fungal colonies were identified using colony morphology, gram staining, and standard microbial tests. Chi-square test, PCA and linear mixed model were run by SPSS version 24.0 for data analysis. Results The highest bacterial contaminations were found in the burns ward (294 CFU/m(3)), operating theater (147 CFU/m(3)), and emergency department (124 CFU/m(3)), respectively. Fungal contamination was higher in the derm ward (110 CFU/m(3)) than other sampling sites. The dominant genus of gram-positive bacteria wasStaphylococcus epidermidis(n = 60, 62.5%) and the dominant genus of gram-negative bacteria was Citrobacter freundi (n = 11, 11.5%). The most fungal gens isolated from the hospital air samples were Penicillium (n = 73, 76%), Alternaria (n = 51, 53.1%), Aspergillus niger (n = 40, 41.7%), and Aspergillus flavus (n = 34, 35.4%), respectively. Conclusion Considering that the burn wounds represent a susceptible site for opportunistic microorganisms, even low concentration of fungi/bacteria in air can be considered as arisk factor that facilitates transmission of the infectiousagents in the hospital. Therefore, control measures should be taken to reduce the infection hazard in health staff and patients. These measures include ensuring effective ventilation, cleaning and decontaminating surfaces and equipment, restricting the personnel and patient companions' movement across the wards.