Rectal swab samples from healthy (92) and diarrheic (44) dogs were analyzed in order to characterize canine gut microbiota. Isolation and identification of microbiota was carried out by conventional culture methods. Gut microbiota isolated include E. coli (65.2% incidence in healthy versus 75% in diarrheic dogs), Proteus (61.9% vs. 65.9%), Enterobacter (26% vs. 11.3%), Klebsiella (26% vs. 20.4%) and Pseudomonas (28.2% vs. 45.4%) species. E. coli isolates were further confirmed by PCR targeting E16S gene. Serological typing of PCR confirmed E. coli (93) revealed rough (19 isolates), O141 (5 isolates), O128 (2 isolates), O9 (2 isolates), O126 (2 isolates), O15, O20, O35, O49, O63, O85, O101, O116, O117, O118, O119 (1 isolate each) serotypes and 52 isolates were found to be ‘O’ group untypable (UT). The present study revealed the occurrence of Enteropathogenic (O49, O118, O119, O126, and O128) and Enterotoxigenic (O15) strains of E. coli in dogs.