A method was developed whereby high quality FTIR spectra could be rapidly acquired from soil-borne filamentous cyanobacteria using ATR FTIR spectroscopy. Spectra of all strains displayed bands typical of those previously reported for microalgae and water-borne cyanobacteria, with each strain having a unique spectral profile. Most variation between strains occurred in the Ca??O stretching and the amide regions. Soft Independent Modelling by Class Analogy (SIMCA) was used to classify the strains with an accuracy of better than 93 , with best classification results using the spectral region from 1800a??950 cma??1. Despite this spectral region undergoing substantial changes, particularly in amide and Ca??O stretching bands, as cultures progressed through the early-, mid- to late-exponential growth phases, classification accuracy was still good (a??80 ) with data from all growth phases combined. These results indicate that ATR/FTIR spectroscopy combined with chemometric classification methods constitute a rapid, reproducible, and potentially automated approach to classifying soil-borne filamentous cyanobacteria.