Antibiotics and the genetic elements that confer resistance to them are simultaneously released into aquatic environments via human waste streams and agricultural run-off. These antibiotics persist at low, but biologically relevant, concentrations that could induce a general increase in the frequency of point mutations, recombination, and lateral gene transfer via the SOS response. Here we examined the response of Pseudomonas aeruginosa and Pseudomonas protegens to sub-clinical levels of the antibiotics kanamycin, tetracycline and ciprofloxacin. Single bacterial colonies were serially streaked onto media containing 1/10 the minimum inhibitory concentration (MIC) of each antibiotic. Serial transfers were then maintained over 40 generations. To monitor for possible cross-contamination of cultures, we performed ERIC and BOX PCR every five generations. To our surprise, significant alterations to the PCR fingerprints were detectable after only five transfers, suggesting indels, transpositions, or point mutations had altered the PCR targets in the experimental lines. No such changes occurred in control lines. Experimental lines also displayed variant colony morphologies by generation 40. Final MICs were significantly higher in some experimental lines of Ps. protegens, suggesting that 1/10 the MIC was sufficient to select for antibiotic resistance. The implications of these results are clear: Exposure of the environmental microbiome to low level antibiotic pollution will induce genomic changes, including the potential to generate newly resistant species that may be of significant concern for human health.