The study aimed to assess the black staining found on the facing stone of the National Museum of the American Indian (NMAI) building through a molecular characterization of the microbial communities of three samples. The samples were: #2 from the low wall by the loading dock at the north-west corner of the NMAI building; #5 in correspondence with the runoff from the scupper on the east wall of the roof near the Senator Daniel K. Inouye Terrace, and #7 from the same east wall but from the lowest ashlar. Bacteria, cyanobacteria, eukaryotic algae and fungi were studied by several techniques, such as Denaturing Gradient Gel Electrophoresis (DGGE), principal component analysis applied to the DGGE profiles, and gene sequencing.