A survey method is described for sampling and identifying bacterial genera associated with the seasonal population of bacteria on cotton grown in Florence and for different cotton growing regions. The method utilizes the MIDI Microbial Identification System (MIS) which uses whole cell fatty acid analysis by gas chromatography. A gram-index concept is introduced. Initial results support previous findings that California cottons generally contain low levels of endotoxin and gram-negative bacteria and that Mississippi cottons generally contain high levels of endotoxin and gram-negative bacteria. In California cottons, the bulk of gram-positive species consisted of Bacillus spp.; and in Mississippi and Texas region cottons, the bulk of gram-negative species was made up of Pseudomonas spp.