Soils have a long history as trace evidence. Their chemical, physical and biological properties can be used to trace the movement of people and objects for forensic science purposes. More recently the molecular biology of soils has become of interest as trace evidence. However, before the molecular analysis of soils can be implemented into court systems the putative changes to soil fingerprints due to storage and handling of soil samples must be determined. To this end, soil samples were collected seasonally from a depth of 0 to 5 cm at four different locations in Nebraska. These locations represented soils of contrasting texture and organic matter. Composite soil samples from each location were then divided into subsamples. Microbial DNA and fatty acids from the first subsample were extracted immediately (fresh), while the other subsamples went through a selected storage treatment under varying conditions (-80¢ªC, -20¢ªC, 4¢ªC, lyophilized, air dried, oven dried) for five weeks. In addition, fresh samples (revisited) were collected 14 days later from the site and processed in the same manner. The polymerase chain reaction (PCR) was used to amplify and fluorescently tag amplicons from the 16S rRNA gene. The PCR products were processed using capillary electrophoresis-single strand conformation polymorphism (CE-SSCP). Fatty acid methyl ester (FAME) analysis was used as a second method to fingerprint soil samples. CE-SSCP and FAME analyses capture the diversity and structure of the microbial community within an individual soil sample. The effectiveness of these analytical methods to detect small variations in the soil microbial community significant to forensic trace evidence will be discussed.