Microbial migration between the ear, throat, and nasal cavities can aggravate certain otorhinolaryngological conditions. For instance, Staphylococcus aureus colonization in the middle ear increases otitis media occurrence, while nasal colonization can exacerbate allergic rhinitis (AR) symptoms. S. aureus produces superantigens (SAgs) that include T-cell SAgs (e.g. staphylococcal enterotoxins SEA, SEB, SEC, and SED), which cross-link class II major histocompatibility complex (MHC) molecules on antigen-presenting cells with T-cell receptors, causing widespread T-cell activation and cytokine release. It also produces B-cell superantigens, such as Protein A (SpA), which bind to immunoglobulins and activate B-cells, contributing to allergic airway diseases. The detection of these SAg genes and methicillin-resistant Staphylococcus aureus (MRSA) marker genes (mecA and femB) in both allergic and healthy individuals may enable the assessment of microbial transmission risk between the ear and nose. In this study, we quantified five SAg genes (SEA, SEB, SEC, SED, and SpA) and the MRSA markers mecA and femB using quantitative PCR (qPCR) in swab samples from 11 healthy individuals and one AR patient. The results demonstrated that these genes were not always co-present or correlated between an individual’s ear and nose samples. In several cases, MRSA marker genes were detected by qPCR despite the absence of S. aureus growth on selective culture, indicating potential detection of other carriers of these genes. These findings underscore the importance of quantifying SAg and MRSA gene levels in the ear and nose to establish baseline colonization and to assess potential risk factors for related otorhinolaryngological conditions.