This research analyzed the effect of fecal contamination caused by sewage, and its relationship with the presence of enteropathogenic strains of Escherichia coli in the feces of South American sea lions (Otaria flavescens) from Iquique Bay and surrounding waters. The E. coli strains isolated from the water column of the bay and sewage outlet, showed the presence of the gene eae. In the strains isolated from the feces of both sea lion colonies no presence of virulent diarrheagenic genes was detected. The genotyping of strains resulted in clusters according to their origin and showed separation of the samples of E. coli population of the colonies of sea lions and those of the strains isolated from the column water of Iquique Bay.