The presence of Escherichia coli in drinking water is an indication of fecal contamination and can represent a risk of waterborne diseases. Forty-nine E.coli strains isolated from different sources of drinking water (distribution system, well, spring and mineral water) were placed into the phylogenetic groups A (15 strains), B1 (19 strains), B2 (2 strains) and D (13 strains). Approximately 30% of the strains analyzed belonged to groups B2 and D, which usually include potentially extraintestinal pathogenic strains. Moreover, the assignment of the strains to different phylogenetic groups indicates that different contamination events occurred in these waters. These results were compared with the distribution of E. coli strains isolated from two rivers and two dams into the phylogenetic groups. A significant difference was observed when the distribution of drinking water strains into the phylogenetic groups was compared to the results obtained from the Guarapiranga Dam and the Jaguari and Sorocaba Rivers. The results obtained in this work suggest that PCR-based methods can be used for a rapid assessment of potentially pathogenic E. coli strains in water samples.