Avian colibacillosis is considered a major bacterial disease in the poultry industry worldwide and one of the most common avian diseases that communicable to human. A prevalence study on APEC was carried out on 56 cloacal swabs isolated from 17 weeks old ducks suffering from diarrhea. The isolates were cultured onto MacConkey and EMB agar for isolation and identification of E. coli followed by serotyping then PCR for the detection of virulence encoding genes (iss, fimH, eaeA, tsh, ibeA, stx1and stx2) and their phylogenetic group. The collected data showed that, out of 56 isolates 12 isolates were typical APEC commonly belong to7 different serogroups and having at least two virulence genes. The data demonstrated that, iss and fimH encoding genes were present in all the examined serogroups (100%). In contrast stx1 and eaeA were absent in all isolates, while tsh and ibeA were variable (63.63%, 27.27%), respectively. The presented phylogenetic groups were A and B1 in percentage of 27.27% and 72.72%, respectively. The use of phylogenetic groups makes a revolution in the identification of APEC which enhanced our knowledge for APEC pathogenicity and helping pave the road for the application of the suitable preventive and curative measures in order to reduce the economic drawbacks of avian colibacillosis in large-scale farms.