The International Space Station (ISS) is a huge manned construct located approximately 400 km above the earth and is inhabited by astronauts performing space experiments. Because the station is within a closed microgravity environment, the astronauts are subject to consistent stress. This study analyzed the temporal changes in the skin fungal microbiota of 10 astronauts using pyrosequencing and quantitative PCR assay before, during, and after their stay in the ISS. Lipophilic skin fungi, Malassezia predominated most samples regardless of the collection period, body site (cheek or chest), or subject. During their stay in the ISS, the level of Malassezia colonization changed by 7.6- +/- 7.5-fold (mean +/- standard deviation) and 9.5- +/- 24.2-fold in cheek and chest samples, respectively. At the species level, M. restricta, M. globosa, and M. sympodialis were more abundant. In the chest samples, the ratio of M. restricta to all Malassezia species increased, whereas it did not change considerably in cheek samples. Fungal diversity was reduced, and the ratio of Malassezia to all fungal colonization increased during the astronauts’ stay at the ISS. The ascomycetous yeast Cyberlindnera jadinii was detected in abundance in the in-flight sample of 5 of the 10 astronauts. The microorganism may have incidentally adhered to the skin during the preflight period and persisted on the skin thereafter. This observation suggests the ability of a specific or uncommon microorganism to proliferate in a closed environment. Our study is the first to reveal temporal changes in the skin fungal microbiota of ISS astronauts. These findings will provide information useful for maintaining the health of astronauts staying in the space environment for long periods and for preventing infection due to the human skin microbiota.