Abstract: In a method and apparatus for identifying and distinguishing fungal species, a hyperspectral imaging scanner is used to acquire hyperspectral image data for radiation obtained from a sample area in which at least one unknown fungal species is present. A computer compares the acquired hyperspectral image data with spectral signature data stored in a digital library, which includes spectral signature data for each one of a group of known fungal species, and identifies the fungal species, based on the result of such comparison. The spectral signature data stored in the digital library take into account, for each fungal species, spectral variations that can occur due to at least one of environmental and temporal influences. The computer comparison includes a pixel-by-pixel analysis of the degree of difference between acquired hyperspectral image data and the spectral signature data, so that a spatial distribution of identified fungal species can be determined for a sample area.