Corrosion of aluminium (Al) is a potential problem for spacecraft as this metal is used for various mechanical parts due to its strength, durability, etc. However, it can be corroded by certain factors including microbes. Studying microbes which can be implicated in microbiologically influenced corrosion (MIC) due to their extremophilic nature is of vital importance. In this current study, Al and acid-tolerant microbes were isolated from the samples of China space station assembly cleanroom surfaces; acidic environments can accelerate the corrosion process on metal surfaces. Nine bacterial and 10 fungal strains were identified with 16S ribosomal RNA gene/internal transcribed spacer region sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The dominant bacteria were of Bacillus, fungi of Penicillium and Aspergillus genera. Knowing the microbes which may be conveyed from the cleanrooms to the space stations with a potential capacity of Al degradation is important for long-term maintenance of station components. This study might aid in designing further researches of the aforementioned microorganisms and, therefore, contribute to the prevention of MIC.