The intensive use of cephalosporins is considered to cause faecal colonization of Escherichia coli producing the extended spectrum beta-lactamase ( ESBL) and AmpC beta-lactamase. The aim of the study was to determinate the prevalence and distribution of the genes encoding ESBL and AmpC beta-lactamase in E. coli isolates collected from faeces of healthy dogs (n=192) and cats (n=192) in Istanbul. Production of ESBL and AmpC enzymes was phenotypically detected by screening and confirmatory tests. Some of the ESBL (TEM, SHV, OXA-10, PER-2, CTX-M groups) and AmpC genes (CIT, FOX, MOX, EBC, ACC, DHA) were investigated by PCR. The prevalence of ESBL producing E. coli was demonstrated 20.3% (n=39) in dogs and 8.3% (n=16) in cats; AmpC producing E. coli 3.7% (n=7) in dogs and 0.6% (n=1) in cats. Canine and feline isolates contained bla(CTX-M) Group 1, bla(TEM), bla(CIT), bla(SHV), bla(CTX-M) Group 9 and bla(MOX). Dogs had a increased risk of carrying ESBL and AmpC producing faecal E. coli isolates when compared to the cats (P=0.0008). A canine isolate contained the bla(MOX) AmpC gene, which was previously only reported in humans.