The significant portion of time spent indoors in modern society underscores the importance of indoor air quality for human health. In modern houses, health complications linked to microorganisms such as mold are escalating. Thus, effective microbial control methods are required. A comprehensive understanding remains elusive despite various hypotheses regarding microbial growth influencers, encompassing environmental (ex. Temperature, relative humidity) and anthropogenic factors (ex. Ventilation, air conditioning). This study aimed to elucidate the influence of these factors on microbial communities in two housing types, a traditional Japanese thatched house and a modern reinforced concrete house, both of which are designed to have active openings for ventilation. Environmental parameters (temperature and relative humidity) were monitored, and microbial samples were collected from diverse sites, including floor surfaces, air, and the skin of occupants. Subsequent eukaryotic 18S rRNA gene sequences were obtained by Illumina Miseq sequencing, facilitated the analysis of fungal communities and eukaryotic diversity. A key finding revealed that more humid indoor locations tended to have a higher abundance of Cladosporium, a hygroscopic fungus. And also, in a traditional house with low airtightness and frequent ventilation, the fungal communities in the outdoor and indoor air were relatively similar during the summer, while in a modern house, they were different. This study's findings contribute to an understanding of microbial dynamics in varied residential environments, offering implications for indoor microbial management and public health in the context of architectural design and lifestyle practices.