This study aimed to obtain basic information on the indoor environmental hygiene of non-disinfected libraries used for paper records preservation in the Nara Repository of National Archives, Korea. Microorganisms were investigated in dust samples collected from bookshelves of five libraries using the swab method. Bacterial concentration ranged from 6 CFU/m2 up to 1,730 CFU/m2 . A total of 11 bacterial species belonging to five genera were identified, with Bacillus being the predominant genus. Some bacterial species forming colonies with pigmentation on TSA media were also present. No bacterial species capable of producing cellulases were found. However, one species that could have harmful effects on human health was discovered. For fungi, concentration ranged between 6 CFU/m2 to 1,660 CFU/m2, and a total of six fungal species belonging to five genera were found. Some fungal species forming pigmented colonies on PDA media were also present. Additionally, three species that could have harmful effects on human health were identified. This study’s data suggests that microbial contamination in the dust is relatively low, but the dust in the bookshelves of non-disinfected libraries at the Nara Repository requires management. This is the first report conducted on microorganisms in the dust of bookshelves at the National Archives in Korea.