Indoor fungal communities, found in household dust, significantly influence indoor air quality and health. These communities are shaped by environmental, socioeconomic, and household factors. However, studies on indoor mycobiomes, particularly in Croatia, remain limited. This study investigates the relationship between environmental and household factors and indoor fungal communities, focusing on their diversity, composition, and potential health impacts in Croatian households. Dust samples from 66 Croatian households were analyzed using fungal ITS sequencing. Statistical analyses, including alpha diversity measures, were conducted to evaluate the influence of variables such as pet ownership, number of siblings, and cleaning habits on fungal diversity and abundance. Dominant genera included Malassezia, Cladosporium, and the family Didymosphaeriaceae. Pet ownership and sibling presence were linked to higher fungal diversity, with outdoor-associated genera such as Aureobasidium being more abundant in these households. Cleaning practices selectively altered fungal communities, with frequent cleaning reducing diversity, but not eliminating resilient taxa like Malassezia. This study highlights the interplay between environmental, household, and socioeconomic factors in shaping indoor fungal communities. The findings underscore the importance of addressing indoor fungal diversity to improve air quality and health, particularly in households with vulnerable populations.

Poor indoor air quality is linked to respiratory symptoms and disease, but interactions between indoor pollutants and microbial communities remain unclear. Evidence suggests microorganisms can interact with polycyclic aromatic hydrocarbons (PAHs) through degradation or attachment, potentially shaping indoor microbiomes. In the COPSACsevere cohort, we analyzed bed dust from 84 children (58 asthma, 26 controls). PAHs were measured by HPLC-FLD and microbiota profiled by 16S rRNA and ITS2 sequencing. Questionnaires captured sociodemographic and lifestyle factors. Associations were tested using PERMANOVA, Spearman correlations, and MaAsLin2. Bacterial community composition varied with the host factors age, sex, and parental education, but showed no association with PAH concentrations. Fungal diversity and composition were significantly associated with PAHs, especially pyrene and fluoranthene, which explained 6.1–6.3% variance (p < 0.05) and were positively correlated with Shannon diversity and evenness. Several fungal taxa including Lecanoraceae, Helotiales, and Circinaria correlated positively with PAHs. Asthma status was not associated with bacterial or fungal alpha and beta diversity metrics. PAHs selectively influenced fungal but not bacterial communities in bed dust. Although no asthma associations were detected and no mechanisms can be inferred, these findings highlight potential chemical–fungal interactions in indoor environments and their relevance for future respiratory health research. These results suggest that chemical exposures may shape specific components of indoor microbiomes independent of host disease status, emphasizing the need to integrate chemical–biological interactions in indoor exposure assessments in future environmental health studies and interventions.