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A total of 724 Escherichia coli isolates sampled from 38 wild bottlenose dolphins (Tursiops truncatus) from the Charleston Harbor area, South Carolina, and the Indian River Lagoon, Florida, were screened for resistance to 25 antibiotics. The percentages of animals harboring at least one resistant isolate differed significantly between sampling locations. No resistance was detected in E. coli from dolphins at either site for six of the 25 antibiotics tested. Resistance to penicillin was most common followed by cephalothin, ampicillin, and amoxicillin. Within-animal isolate variability was examined in addition to between sampling locale. Isolates from animals sampled in the Charleston Harbor area exhibited a greater complexity of resistance patterns and within individual diversity compared to isolates sampled from animals in the Indian River Lagoon. Causes related to the observed heterogeneity are discussed.