Repetitive element PCR (rep-PCR) DNA fingerprinting is a cultivation-dependent technique that can be used to differentiate strains within a bacterial species.  Highly specific genomic “fingerprints” are generated and have proven useful in differentiating among various strains of fecal indicator bacteria including E. coli.  We employed a PCR primer (BOX A1R) corresponding to interspersed repetitive DNA elements which occur in variable locations throughout the bacterial genome.  The objective of the present study was to analyze rep-PCR fingerprints of 400 E. coli isolates from conventional and organic sheep and poultry production systems, as well as 360 isolates from forage finished beef cattle.  The technique was also employed to examine the persistence of E. coli in the soil of grazing areas impacted by animal wastes.  The working hypothesis was that there would be differences in these fingerprint patterns related to source, with greater commonality of fingerprints within groups than between groups.  We reasoned that with time fingerprints of E. coli isolates obtained from impacted soils would become more like those of the grazing animals.  Rectal swabs were collected from 20 organically and conventionally reared sheep and chickens and fecal samples from 36 winter pastured beef calves at the WVU farms in Morgantown, WV.  rep-PCR was performed on isolates and multiple PCR products were separated by electrophoresis.  Banding patterns were assigned strain identities and similarities among strains were investigated by UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis.  Data support the presence of multiple E. coli strains among the various animals and suggest that distinct strains are obtained based on the production practice employed, which in turn affects populations and persistence of E. coli in soils.