Little is known about the factors influencing the abundance and community composition of airborne biotic contaminants in swine confinement buildings (SCBs). Microbial air samples were collected from three different SCBs equipped with three different types of manure removal systems (deep-pit manure removal with slats, scraper removal system, and deep-litter bed system). The abundance and composition of airborne biotic contaminants of all the collected air samples were analyzed using cultivation-independent methods. The V1-V3 region of the 16S rRNA gene was amplified from the extracted DNA and sequenced using 454-pyrosequencing. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were quantified using real-time PCR. The abundance of 16S rRNA gene and tetracycline resistance genes were significantly higher in SCBs equipped with a deep-pit manure removal system with slats, except for tetB gene. This contrasts with the opposite trend found previously by culture-based studies. The aerial bacterial community composition, as measured by pairwise Bray-Curtis distances, varied significantly according to the manure removal system. 16S rRNA-based pyrosequencing revealed Firmicutes (72.4%) as the dominant group with Lactobacillus as the major genus, while Actinobacteria constituted 10.7% of the detectable bacteria. Firmicutes were more abundant in SCBs with deep pit with slats, whereas Actinobacteria were highly abundant in SCBs with a deep-litter bed system. Overall, the results of this study suggest that the manure removal system plays a key role in structuring the abundance and composition of airborne biotic contaminants in SCBs.