Environmental fungi can damage the documentary heritage conserved in archives and affect the personnel’s health if their concentrations, thermohygrometric parameters and ventilation conditions are not adequate, problems that can be accentuated by Climate Change. The aims of this work were to identify and to characterize the airborne fungal pollution of naturally ventilated repositories in the Provincial Historical Archive of Santiago de Cuba and predict the risk that these fungi pose to the staff’s health. Indoor air of three repositories of this archive and the outdoor air were sampled in an occasion every time in 2015, 2016 and 2017 using a SAS sampler. The obtained fungal concentrations varied from 135.6 CFU/m3 to 421.1 CFU/m3 and the indoor/outdoor ratios fluctuated from 0.7 to 4.2, evidencing a variable environmental quality over time, but in the third sampling the repositories environments showed good quality. Aspergillus and Cladosporium were the predominant genera in these environments. A. flavus was a prevailed species in indoor air, while A. niger and Cl. cladosporioides were the species that showed the greatest similarities with the outdoor air. Coremiella and Talaromyces genera as well as the species Aspergillus uvarum, Alternaria ricini and Cladosporium staurophorum were the first findings for environments of Cuban archives. Xerophilic species (A. flavus, A. niger, A. ochraceus, A. ustus) indicators of moisture problems in the repositories were detected; they are also opportunistic pathogens and toxigenic species but their concentrations were higher than the recommended, demonstrating the potential risk to which the archive personnel is exposed in a circumstantial way.