The scope of this study was to establish the genomic diversity existing between Escherichia coli isolates obtained from water samples retrieved from Arroio Feijó, southern Brazil, using the repetitive extragenic palindromic elements-polymerase chain reaction protocol. Ninety-eight different isolates were identified from samples obtained from five sites. Eleven different clusters presenting identical fingerprinting patterns were detected. The dendrogram contained 28 clusters for 70% similarity cut-off. These clusters enabled the observation of 16 single patterns. The results enabled the observation of genetic diversity between isolates obtained in one sampling site, and those from other sampling sites. Site 5 showed the highest diversity (Shannon–Weaver, H′=2.92) and site 3 exhibited the lowest diversity degree (Shannon–Weaver, H′=2.16).