The objectives of this study were to determine if agricultural soils can be differentiated on the basis of their microbial community DNA fingerprints, and to compare different approaches for analyzing data describing microbial communities. Twenty-eight California agricultural soil samples were collected during 1997-1998 in the San Joaquín Valley. The soils were sampled under cotton, tomato, almond, grape, and safflower crops with the intent to determine microbial variability within one field, between fields of the same crop, and between fields of different crops. All samples were analyzed for sand, silt, clay, nitrogen, inorganic carbon, organic carbon, total carbon, pH and electrical conductivity. Intergenic transcribed spacer (ITS) analysis of polymerase chain reaction (PCR)-amplified community DNA was performed on all samples. The DNA fingerprints were consistently reproducible for a given soil. The bacterial DNA fingerprints (having from 25-30 bands) were more complex than eucaryotic fingerprints (3-12 bands). In general, the variability of microbial community fingerprints in samples collected from the same field was low, compared to samples from other fields, crops, or soil textures, indicating that soils could be differentiated on the basis of their microbial communities. Crop type was strongly related to microbial community composition in some instances; e.g., most almond sample microbial communities grouped separately from those of all other crops. However, in other crops there was considerable variability among samples that had been collected from under the same crop but from different locations in the valley. There were no strong relationships between community composition and soil texture. In some (but not all) cases, samples from different crops that had been collected in the same vicinity had similar fingerprints. Both cluster analysis and principal component analysis (PCA) of the data gave comparable results. Future statistical analyses will determine any relationships between microbial community composition and other soil parameters.