Escherichia coli, a Gram-negative rod organism and the commonest urinary pathogen causing 60-90% of Urinary infections. Two virulence genes (Pap C and hlyA) had been reported to be involved in Escherichia coli pathogenicity and its resistance to antibiotics. The study aimed at detecting PapC and hlyA in E. coli isolated from clinical specimens in two main Tertiary hospitals (Federal Medical Centre and Niger Delta University Teaching Hospital) in Bayelsa State. One hundred and forty-five specimens were collected and analyzed using the standard Bacteriological technique. Antibiotics Susceptibility testing was carried out using the Kirby Bauer method and Polymerase Chain Reaction (PCR) was employed using ABI 970 amplified Biosystem thermal cycler. The susceptibility pattern showed that 18(90%) isolates were resistant to Nalixidic acid, 16(80%) to Ampicillin, 15(75%) to Ceporex, 14(70%) to Septrin and Augmentin, 12(60%) to Reflacine, 11(55%) to Ciprofloxacin, 9(45%) to Gentamycin, 8(40%) to Tarivid and 4(20%) to Streptomycin. Fifteen PCR products were resolved on 1.0% agarose gel, out of which 8(53.3%) harboured Pap C while 1(6.7%) harboured hlyA. Seven of the eight Pap C-carrying isolates were susceptible to Ciprofloxacin while the HlyA virulence gene enhances the resistance of the organism to Ciprofloxacin. Therefore, the E. coli Pap C gene may be incorporated into Ciprofloxacin production to curb antibiotic resistance.