© 2015, Springer Science+Business Media Dordrecht. The aim of this study was to identify the types and abundance of airborne bacteria of two health institutions (1 and 2) and to determine the genetic association between environmental and clinical isolates of Staphylococcus spp. Environmental sampling in institutions 1 and 2 was conducted for 1 year (dry and rainy seasons) using M Air T sampler. The bacteria and their susceptibility to antibiotics were identified. The colony-forming units per cubic meter (CFU/m3) of air were quantified for all the isolates, and the diversity and abundance of species were calculated. The genetic relationship between the clinical and environmental isolates of S. aureus obtained from institution 1 was established by the UPGMA based on RAPD markers. At both of the institutions, the genera most frequently isolated were Staphylococcus and Bacillus, and the greater concentration of airborne bacteria was detected during the dry season than the rainy season. The lowest diversity and highest dominance was found in the institution 2. On the other hand, at institution 1, the genus that was resistant to antibiotics was Staphylococcus, whereas at institution 2, no isolate was found to be resistant to antibiotics. Furthermore, no association between the clinical and environmental isolates of S. aureus was found. However, one clone was found in different areas of the institution 1. The presence of airborne pathogenic bacteria in institutions 1 and 2 is important to establish the measures for the prevention and control of nosocomial outbreaks.