Respiratory health outcomes including asthma and allergy can be influenced by indoor microbiome, which is ultimately shaped by home characteristics. The objective of this study was to investigate the concentration of Stenotrophomonas maltophilia, an emerging global pathogen, in air and dust samples. Forty-two homes were selected from the birth cohort of Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS) based on home moldiness as measured using Environmental Relative Moldiness Index (ERMI). House dust was collected by floor vacuuming and sieved with a 355 µm mesh screen. Air samples were taken over a 24-hr period using a NIOSH 2-stage cyclone sampler, which collected airborne particles in three size fractions: <1.0 micro-meter, 1.0 – 1.8 micro-meter, and > 1.8 micro-meter. Bacterial DNA was extracted and S. maltophilia was quantified using a quantitative PCR assay with bacteria-specific primers and TaqMan probe. The S. maltophilia concentrations in indoor dust were greater in homes with high ERMI (p = 0.017). Highest concentrations of airborne S. maltophilia were measured in the size range of >1.8 micro-meter, indicating likely aggregation of the bacterial cells with typical physical size of 0.5 to 1.5 micro-meter in length. S. maltophilia dust concentrations were correlated with concentrations measured in air samples in the 1.0 – 1.8 micro-meter size fraction (r = 0.480, p =0.003) as well as with the total airborne concentration (all three size fractions combined) (r = 0.374, p = 0.025). Associations between indoor molds (as well as ERMI) and bacteria are relatively unknown. S. maltophilia is the first bacterial species associated with higher ERMI values in homes. The association of S. maltophilia with high concentrations of indoor fungi may be related to its chitinase production. These enzymes allow the bacterium to utilize chitin, a structural component of the cell wall of fungi, algae, and the exoskeleton of insects.